id sid tid token lemma pos 10_1101-2020_10_26_351783 1 1 A a DT 10_1101-2020_10_26_351783 1 2 validated validate VBN 10_1101-2020_10_26_351783 1 3 generally generally RB 10_1101-2020_10_26_351783 1 4 applicable applicable JJ 10_1101-2020_10_26_351783 1 5 approach approach NN 10_1101-2020_10_26_351783 1 6 using use VBG 10_1101-2020_10_26_351783 1 7 the the DT 10_1101-2020_10_26_351783 1 8 systematic systematic JJ 10_1101-2020_10_26_351783 1 9 assessment assessment NN 10_1101-2020_10_26_351783 1 10 of of IN 10_1101-2020_10_26_351783 1 11 disease disease NN 10_1101-2020_10_26_351783 1 12 modules module NNS 10_1101-2020_10_26_351783 1 13 by by IN 10_1101-2020_10_26_351783 1 14 GWAS GWAS NNP 10_1101-2020_10_26_351783 1 15 reveals reveal VBZ 10_1101-2020_10_26_351783 1 16 a a DT 10_1101-2020_10_26_351783 1 17 multi multi JJ 10_1101-2020_10_26_351783 1 18 - - JJ 10_1101-2020_10_26_351783 1 19 omic omic JJ 10_1101-2020_10_26_351783 1 20 module module NN 10_1101-2020_10_26_351783 1 21 strongly strongly RB 10_1101-2020_10_26_351783 1 22 associated associate VBN 10_1101-2020_10_26_351783 1 23 with with IN 10_1101-2020_10_26_351783 1 24 risk risk NN 10_1101-2020_10_26_351783 1 25 factors factor NNS 10_1101-2020_10_26_351783 1 26 in in IN 10_1101-2020_10_26_351783 1 27 multiple multiple JJ 10_1101-2020_10_26_351783 1 28 sclerosis sclerosis NN 10_1101-2020_10_26_351783 1 29 1 1 CD 10_1101-2020_10_26_351783 1 30 A a DT 10_1101-2020_10_26_351783 1 31 validated validate VBN 10_1101-2020_10_26_351783 1 32 generally generally RB 10_1101-2020_10_26_351783 1 33 applicable applicable JJ 10_1101-2020_10_26_351783 1 34 approach approach NN 10_1101-2020_10_26_351783 1 35 using use VBG 10_1101-2020_10_26_351783 1 36 the the DT 10_1101-2020_10_26_351783 1 37 systematic systematic JJ 10_1101-2020_10_26_351783 1 38 assessment assessment NN 10_1101-2020_10_26_351783 1 39 of of IN 10_1101-2020_10_26_351783 1 40 disease disease NN 10_1101-2020_10_26_351783 1 41 modules module NNS 10_1101-2020_10_26_351783 1 42 by by IN 10_1101-2020_10_26_351783 1 43 GWAS GWAS NNP 10_1101-2020_10_26_351783 1 44 reveals reveal VBZ 10_1101-2020_10_26_351783 1 45 a a DT 10_1101-2020_10_26_351783 1 46 multi multi JJ 10_1101-2020_10_26_351783 1 47 - - JJ 10_1101-2020_10_26_351783 1 48 omic omic JJ 10_1101-2020_10_26_351783 1 49 module module NN 10_1101-2020_10_26_351783 1 50 strongly strongly RB 10_1101-2020_10_26_351783 1 51 associated associate VBN 10_1101-2020_10_26_351783 1 52 with with IN 10_1101-2020_10_26_351783 1 53 risk risk NN 10_1101-2020_10_26_351783 1 54 factors factor NNS 10_1101-2020_10_26_351783 1 55 in in IN 10_1101-2020_10_26_351783 1 56 multiple multiple JJ 10_1101-2020_10_26_351783 1 57 sclerosis sclerosis NN 10_1101-2020_10_26_351783 1 58 Tejaswi Tejaswi NNP 10_1101-2020_10_26_351783 1 59 V.S. V.S. NNP 10_1101-2020_10_26_351783 2 1 Badam1,2† badam1,2† UH 10_1101-2020_10_26_351783 2 2 , , , 10_1101-2020_10_26_351783 2 3 Hendrik Hendrik NNP 10_1101-2020_10_26_351783 2 4 A. A. NNP 10_1101-2020_10_26_351783 2 5 de de NNP 10_1101-2020_10_26_351783 2 6 Weerd1,2† Weerd1,2† NNP 10_1101-2020_10_26_351783 2 7 , , , 10_1101-2020_10_26_351783 2 8 David David NNP 10_1101-2020_10_26_351783 2 9 Martínez Martínez NNP 10_1101-2020_10_26_351783 2 10 - - HYPH 10_1101-2020_10_26_351783 2 11 Enguita2 Enguita2 NNP 10_1101-2020_10_26_351783 2 12 , , , 10_1101-2020_10_26_351783 2 13 Tomas Tomas NNP 10_1101-2020_10_26_351783 2 14 Olsson3 Olsson3 NNP 10_1101-2020_10_26_351783 2 15 , , , 10_1101-2020_10_26_351783 2 16 Lars Lars NNP 10_1101-2020_10_26_351783 2 17 Alfredsson3,4,Ingrid Alfredsson3,4,Ingrid NNP 10_1101-2020_10_26_351783 2 18 Kockum3,Maja Kockum3,Maja VBZ 10_1101-2020_10_26_351783 2 19 Jagodic3 Jagodic3 NNP 10_1101-2020_10_26_351783 2 20 , , , 10_1101-2020_10_26_351783 2 21 Zelmina Zelmina NNP 10_1101-2020_10_26_351783 2 22 Lubovac Lubovac NNP 10_1101-2020_10_26_351783 2 23 - - HYPH 10_1101-2020_10_26_351783 2 24 Pilav1 Pilav1 NNP 10_1101-2020_10_26_351783 2 25 * * NFP 10_1101-2020_10_26_351783 2 26 , , , 10_1101-2020_10_26_351783 2 27 Mika Mika NNP 10_1101-2020_10_26_351783 2 28 Gustafsson2 Gustafsson2 NNP 10_1101-2020_10_26_351783 2 29 * * NFP 10_1101-2020_10_26_351783 2 30 1School 1school CD 10_1101-2020_10_26_351783 2 31 of of IN 10_1101-2020_10_26_351783 2 32 Bioscience Bioscience NNP 10_1101-2020_10_26_351783 2 33 , , , 10_1101-2020_10_26_351783 2 34 Systems Systems NNPS 10_1101-2020_10_26_351783 2 35 Biology Biology NNP 10_1101-2020_10_26_351783 2 36 Research Research NNP 10_1101-2020_10_26_351783 2 37 Center Center NNP 10_1101-2020_10_26_351783 2 38 , , , 10_1101-2020_10_26_351783 2 39 University University NNP 10_1101-2020_10_26_351783 2 40 of of IN 10_1101-2020_10_26_351783 2 41 Skövde Skövde NNP 10_1101-2020_10_26_351783 2 42 , , , 10_1101-2020_10_26_351783 2 43 Sweden Sweden NNP 10_1101-2020_10_26_351783 2 44 2Bioinformatics 2Bioinformatics NNP 10_1101-2020_10_26_351783 2 45 , , , 10_1101-2020_10_26_351783 2 46 Department Department NNP 10_1101-2020_10_26_351783 2 47 of of IN 10_1101-2020_10_26_351783 2 48 Physics Physics NNP 10_1101-2020_10_26_351783 2 49 , , , 10_1101-2020_10_26_351783 2 50 Chemistry Chemistry NNP 10_1101-2020_10_26_351783 2 51 and and CC 10_1101-2020_10_26_351783 2 52 Biology Biology NNP 10_1101-2020_10_26_351783 2 53 , , , 10_1101-2020_10_26_351783 2 54 Linköping linköpe VBG 10_1101-2020_10_26_351783 2 55 university university NN 10_1101-2020_10_26_351783 2 56 , , , 10_1101-2020_10_26_351783 2 57 Linköping Linköping NNP 10_1101-2020_10_26_351783 2 58 , , , 10_1101-2020_10_26_351783 2 59 Sweden Sweden NNP 10_1101-2020_10_26_351783 2 60 3Department 3Department NNP 10_1101-2020_10_26_351783 2 61 of of IN 10_1101-2020_10_26_351783 2 62 Clinical Clinical NNP 10_1101-2020_10_26_351783 2 63 Neuroscience Neuroscience NNP 10_1101-2020_10_26_351783 2 64 , , , 10_1101-2020_10_26_351783 2 65 Karolinska Karolinska NNP 10_1101-2020_10_26_351783 2 66 Institutet Institutet NNP 10_1101-2020_10_26_351783 2 67 , , , 10_1101-2020_10_26_351783 2 68 Center Center NNP 10_1101-2020_10_26_351783 2 69 for for IN 10_1101-2020_10_26_351783 2 70 Molecular Molecular NNP 10_1101-2020_10_26_351783 2 71 Medicine Medicine NNP 10_1101-2020_10_26_351783 2 72 , , , 10_1101-2020_10_26_351783 2 73 Karolinska Karolinska NNP 10_1101-2020_10_26_351783 2 74 University University NNP 10_1101-2020_10_26_351783 2 75 Hospital Hospital NNP 10_1101-2020_10_26_351783 2 76 , , , 10_1101-2020_10_26_351783 2 77 SE-171 SE-171 NNP 10_1101-2020_10_26_351783 2 78 76 76 CD 10_1101-2020_10_26_351783 2 79 , , , 10_1101-2020_10_26_351783 2 80 Stockholm Stockholm NNP 10_1101-2020_10_26_351783 2 81 , , , 10_1101-2020_10_26_351783 2 82 Sweden Sweden NNP 10_1101-2020_10_26_351783 2 83 4Institute 4Institute NNP 10_1101-2020_10_26_351783 2 84 of of IN 10_1101-2020_10_26_351783 2 85 Environmental Environmental NNP 10_1101-2020_10_26_351783 2 86 Medicine Medicine NNP 10_1101-2020_10_26_351783 2 87 , , , 10_1101-2020_10_26_351783 2 88 Karolinska Karolinska NNP 10_1101-2020_10_26_351783 2 89 Institutet Institutet NNP 10_1101-2020_10_26_351783 2 90 , , , 10_1101-2020_10_26_351783 2 91 Center Center NNP 10_1101-2020_10_26_351783 2 92 for for IN 10_1101-2020_10_26_351783 2 93 Molecular Molecular NNP 10_1101-2020_10_26_351783 2 94 Medicine Medicine NNP 10_1101-2020_10_26_351783 2 95 , , , 10_1101-2020_10_26_351783 2 96 Karolinska Karolinska NNP 10_1101-2020_10_26_351783 2 97 University University NNP 10_1101-2020_10_26_351783 2 98 Hospital Hospital NNP 10_1101-2020_10_26_351783 2 99 , , , 10_1101-2020_10_26_351783 2 100 SE-171 SE-171 NNP 10_1101-2020_10_26_351783 2 101 76 76 CD 10_1101-2020_10_26_351783 2 102 , , , 10_1101-2020_10_26_351783 2 103 Stockholm Stockholm NNP 10_1101-2020_10_26_351783 2 104 , , , 10_1101-2020_10_26_351783 2 105 Sweden Sweden NNP 10_1101-2020_10_26_351783 2 106 †These †These NNP 10_1101-2020_10_26_351783 2 107 authors author NNS 10_1101-2020_10_26_351783 2 108 contributed contribute VBD 10_1101-2020_10_26_351783 2 109 equally equally RB 10_1101-2020_10_26_351783 2 110 to to IN 10_1101-2020_10_26_351783 2 111 the the DT 10_1101-2020_10_26_351783 2 112 work work NN 10_1101-2020_10_26_351783 2 113 . . . 10_1101-2020_10_26_351783 3 1 * * NFP 10_1101-2020_10_26_351783 3 2 These these DT 10_1101-2020_10_26_351783 3 3 authors author NNS 10_1101-2020_10_26_351783 3 4 share share VBP 10_1101-2020_10_26_351783 3 5 senior senior JJ 10_1101-2020_10_26_351783 3 6 authorship authorship NN 10_1101-2020_10_26_351783 3 7 . . . 10_1101-2020_10_26_351783 4 1 Corresponding correspond VBG 10_1101-2020_10_26_351783 4 2 author author NN 10_1101-2020_10_26_351783 4 3 : : : 10_1101-2020_10_26_351783 4 4 Mika Mika NNP 10_1101-2020_10_26_351783 4 5 Gustafsson Gustafsson NNP 10_1101-2020_10_26_351783 4 6 ( ( -LRB- 10_1101-2020_10_26_351783 4 7 mika.gustafsson@liu.se mika.gustafsson@liu.se NNP 10_1101-2020_10_26_351783 4 8 ) ) -RRB- 10_1101-2020_10_26_351783 4 9 Running run VBG 10_1101-2020_10_26_351783 4 10 Title title NN 10_1101-2020_10_26_351783 4 11 : : : 10_1101-2020_10_26_351783 4 12 Multi multi JJ 10_1101-2020_10_26_351783 4 13 - - JJ 10_1101-2020_10_26_351783 4 14 omic omic JJ 10_1101-2020_10_26_351783 4 15 modules module NNS 10_1101-2020_10_26_351783 4 16 in in IN 10_1101-2020_10_26_351783 4 17 multiple multiple JJ 10_1101-2020_10_26_351783 4 18 sclerosis sclerosis NN 10_1101-2020_10_26_351783 4 19 Keywords Keywords NNPS 10_1101-2020_10_26_351783 4 20 : : : 10_1101-2020_10_26_351783 4 21 Benchmark Benchmark NNP 10_1101-2020_10_26_351783 4 22 , , , 10_1101-2020_10_26_351783 4 23 Multi Multi NNP 10_1101-2020_10_26_351783 4 24 - - NNS 10_1101-2020_10_26_351783 4 25 omics omic NNS 10_1101-2020_10_26_351783 4 26 , , , 10_1101-2020_10_26_351783 4 27 Network Network NNP 10_1101-2020_10_26_351783 4 28 modules module NNS 10_1101-2020_10_26_351783 4 29 , , , 10_1101-2020_10_26_351783 4 30 Multiple Multiple NNP 10_1101-2020_10_26_351783 4 31 Sclerosis Sclerosis NNP 10_1101-2020_10_26_351783 4 32 , , , 10_1101-2020_10_26_351783 4 33 Risk risk NN 10_1101-2020_10_26_351783 4 34 factors factor NNS 10_1101-2020_10_26_351783 4 35 SUMMARY summary NN 10_1101-2020_10_26_351783 4 36 : : : 10_1101-2020_10_26_351783 4 37 Our -PRON- PRP$ 10_1101-2020_10_26_351783 4 38 benchmark benchmark NN 10_1101-2020_10_26_351783 4 39 of of IN 10_1101-2020_10_26_351783 4 40 multi multi JJ 10_1101-2020_10_26_351783 4 41 - - JJ 10_1101-2020_10_26_351783 4 42 omic omic JJ 10_1101-2020_10_26_351783 4 43 modules module NNS 10_1101-2020_10_26_351783 4 44 and and CC 10_1101-2020_10_26_351783 4 45 validated validate VBD 10_1101-2020_10_26_351783 4 46 translational translational JJ 10_1101-2020_10_26_351783 4 47 systems system NNS 10_1101-2020_10_26_351783 4 48 medicine medicine NN 10_1101-2020_10_26_351783 4 49 workflow workflow NN 10_1101-2020_10_26_351783 4 50 for for IN 10_1101-2020_10_26_351783 4 51 dissecting dissect VBG 10_1101-2020_10_26_351783 4 52 complex complex JJ 10_1101-2020_10_26_351783 4 53 diseases disease NNS 10_1101-2020_10_26_351783 4 54 resulted result VBD 10_1101-2020_10_26_351783 4 55 in in IN 10_1101-2020_10_26_351783 4 56 multi multi JJ 10_1101-2020_10_26_351783 4 57 - - JJ 10_1101-2020_10_26_351783 4 58 omic omic JJ 10_1101-2020_10_26_351783 4 59 module module NN 10_1101-2020_10_26_351783 4 60 of of IN 10_1101-2020_10_26_351783 4 61 220 220 CD 10_1101-2020_10_26_351783 4 62 genes gene NNS 10_1101-2020_10_26_351783 4 63 highly highly RB 10_1101-2020_10_26_351783 4 64 enriched enrich VBN 10_1101-2020_10_26_351783 4 65 for for IN 10_1101-2020_10_26_351783 4 66 risk risk NN 10_1101-2020_10_26_351783 4 67 factors factor NNS 10_1101-2020_10_26_351783 4 68 associated associate VBN 10_1101-2020_10_26_351783 4 69 with with IN 10_1101-2020_10_26_351783 4 70 multiple multiple JJ 10_1101-2020_10_26_351783 4 71 sclerosis sclerosis NN 10_1101-2020_10_26_351783 4 72 . . . 10_1101-2020_10_26_351783 5 1 ( ( -LRB- 10_1101-2020_10_26_351783 5 2 which which WDT 10_1101-2020_10_26_351783 5 3 was be VBD 10_1101-2020_10_26_351783 5 4 not not RB 10_1101-2020_10_26_351783 5 5 certified certify VBN 10_1101-2020_10_26_351783 5 6 by by IN 10_1101-2020_10_26_351783 5 7 peer peer NN 10_1101-2020_10_26_351783 5 8 review review NN 10_1101-2020_10_26_351783 5 9 ) ) -RRB- 10_1101-2020_10_26_351783 5 10 is be VBZ 10_1101-2020_10_26_351783 5 11 the the DT 10_1101-2020_10_26_351783 5 12 author author NN 10_1101-2020_10_26_351783 5 13 / / SYM 10_1101-2020_10_26_351783 5 14 funder funder NN 10_1101-2020_10_26_351783 5 15 . . . 10_1101-2020_10_26_351783 6 1 All all DT 10_1101-2020_10_26_351783 6 2 rights right NNS 10_1101-2020_10_26_351783 6 3 reserved reserve VBD 10_1101-2020_10_26_351783 6 4 . . . 10_1101-2020_10_26_351783 7 1 No no DT 10_1101-2020_10_26_351783 7 2 reuse reuse NN 10_1101-2020_10_26_351783 7 3 allowed allow VBN 10_1101-2020_10_26_351783 7 4 without without IN 10_1101-2020_10_26_351783 7 5 permission permission NN 10_1101-2020_10_26_351783 7 6 . . . 10_1101-2020_10_26_351783 8 1 The the DT 10_1101-2020_10_26_351783 8 2 copyright copyright NN 10_1101-2020_10_26_351783 8 3 holder holder NN 10_1101-2020_10_26_351783 8 4 for for IN 10_1101-2020_10_26_351783 8 5 this this DT 10_1101-2020_10_26_351783 8 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 8 7 version version NN 10_1101-2020_10_26_351783 8 8 posted post VBD 10_1101-2020_10_26_351783 8 9 January January NNP 10_1101-2020_10_26_351783 8 10 6 6 CD 10_1101-2020_10_26_351783 8 11 , , , 10_1101-2020_10_26_351783 8 12 2021 2021 CD 10_1101-2020_10_26_351783 8 13 . . . 10_1101-2020_10_26_351783 8 14 ; ; : 10_1101-2020_10_26_351783 8 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 8 16 : : : 10_1101-2020_10_26_351783 8 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 8 18 preprint preprint NN 10_1101-2020_10_26_351783 8 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 8 20 2 2 CD 10_1101-2020_10_26_351783 8 21 ABSTRACT ABSTRACT NNP 10_1101-2020_10_26_351783 8 22 Background background NN 10_1101-2020_10_26_351783 8 23 : : : 10_1101-2020_10_26_351783 8 24 There there EX 10_1101-2020_10_26_351783 8 25 are be VBP 10_1101-2020_10_26_351783 8 26 few few JJ 10_1101-2020_10_26_351783 8 27 ( ( -LRB- 10_1101-2020_10_26_351783 8 28 if if IN 10_1101-2020_10_26_351783 8 29 any any DT 10_1101-2020_10_26_351783 8 30 ) ) -RRB- 10_1101-2020_10_26_351783 8 31 practical practical JJ 10_1101-2020_10_26_351783 8 32 guidelines guideline NNS 10_1101-2020_10_26_351783 8 33 for for IN 10_1101-2020_10_26_351783 8 34 predictive predictive JJ 10_1101-2020_10_26_351783 8 35 and and CC 10_1101-2020_10_26_351783 8 36 falsifiable falsifiable JJ 10_1101-2020_10_26_351783 8 37 multi multi JJ 10_1101-2020_10_26_351783 8 38 - - HYPH 10_1101-2020_10_26_351783 8 39 omics omic NNS 10_1101-2020_10_26_351783 8 40 data datum NNS 10_1101-2020_10_26_351783 8 41 integration integration NN 10_1101-2020_10_26_351783 8 42 that that WDT 10_1101-2020_10_26_351783 8 43 systematically systematically RB 10_1101-2020_10_26_351783 8 44 integrate integrate VB 10_1101-2020_10_26_351783 8 45 existing exist VBG 10_1101-2020_10_26_351783 8 46 knowledge knowledge NN 10_1101-2020_10_26_351783 8 47 . . . 10_1101-2020_10_26_351783 9 1 Disease Disease NNP 10_1101-2020_10_26_351783 9 2 modules module NNS 10_1101-2020_10_26_351783 9 3 are be VBP 10_1101-2020_10_26_351783 9 4 popular popular JJ 10_1101-2020_10_26_351783 9 5 concepts concept NNS 10_1101-2020_10_26_351783 9 6 for for IN 10_1101-2020_10_26_351783 9 7 interpreting interpret VBG 10_1101-2020_10_26_351783 9 8 genome genome NN 10_1101-2020_10_26_351783 9 9 - - HYPH 10_1101-2020_10_26_351783 9 10 wide wide JJ 10_1101-2020_10_26_351783 9 11 studies study NNS 10_1101-2020_10_26_351783 9 12 in in IN 10_1101-2020_10_26_351783 9 13 medicine medicine NN 10_1101-2020_10_26_351783 9 14 but but CC 10_1101-2020_10_26_351783 9 15 have have VBP 10_1101-2020_10_26_351783 9 16 so so RB 10_1101-2020_10_26_351783 9 17 far far RB 10_1101-2020_10_26_351783 9 18 not not RB 10_1101-2020_10_26_351783 9 19 been be VBN 10_1101-2020_10_26_351783 9 20 systematically systematically RB 10_1101-2020_10_26_351783 9 21 evaluated evaluate VBN 10_1101-2020_10_26_351783 9 22 and and CC 10_1101-2020_10_26_351783 9 23 may may MD 10_1101-2020_10_26_351783 9 24 lead lead VB 10_1101-2020_10_26_351783 9 25 to to IN 10_1101-2020_10_26_351783 9 26 corroborating corroborate VBG 10_1101-2020_10_26_351783 9 27 multi multi JJ 10_1101-2020_10_26_351783 9 28 - - JJ 10_1101-2020_10_26_351783 9 29 omic omic JJ 10_1101-2020_10_26_351783 9 30 modules module NNS 10_1101-2020_10_26_351783 9 31 . . . 10_1101-2020_10_26_351783 10 1 Methods method NNS 10_1101-2020_10_26_351783 10 2 : : : 10_1101-2020_10_26_351783 10 3 We -PRON- PRP 10_1101-2020_10_26_351783 10 4 assessed assess VBD 10_1101-2020_10_26_351783 10 5 eight eight CD 10_1101-2020_10_26_351783 10 6 module module JJ 10_1101-2020_10_26_351783 10 7 identification identification NN 10_1101-2020_10_26_351783 10 8 methods method NNS 10_1101-2020_10_26_351783 10 9 in in IN 10_1101-2020_10_26_351783 10 10 57 57 CD 10_1101-2020_10_26_351783 10 11 previously previously RB 10_1101-2020_10_26_351783 10 12 published publish VBN 10_1101-2020_10_26_351783 10 13 expression expression NN 10_1101-2020_10_26_351783 10 14 and and CC 10_1101-2020_10_26_351783 10 15 methylation methylation NN 10_1101-2020_10_26_351783 10 16 studies study NNS 10_1101-2020_10_26_351783 10 17 of of IN 10_1101-2020_10_26_351783 10 18 19 19 CD 10_1101-2020_10_26_351783 10 19 diseases disease NNS 10_1101-2020_10_26_351783 10 20 using use VBG 10_1101-2020_10_26_351783 10 21 GWAS GWAS NNP 10_1101-2020_10_26_351783 10 22 enrichment enrichment NN 10_1101-2020_10_26_351783 10 23 analysis analysis NN 10_1101-2020_10_26_351783 10 24 . . . 10_1101-2020_10_26_351783 11 1 Next next RB 10_1101-2020_10_26_351783 11 2 , , , 10_1101-2020_10_26_351783 11 3 we -PRON- PRP 10_1101-2020_10_26_351783 11 4 applied apply VBD 10_1101-2020_10_26_351783 11 5 the the DT 10_1101-2020_10_26_351783 11 6 same same JJ 10_1101-2020_10_26_351783 11 7 strategy strategy NN 10_1101-2020_10_26_351783 11 8 for for IN 10_1101-2020_10_26_351783 11 9 multi multi JJ 10_1101-2020_10_26_351783 11 10 - - NNS 10_1101-2020_10_26_351783 11 11 omics omic NNS 10_1101-2020_10_26_351783 11 12 integration integration NN 10_1101-2020_10_26_351783 11 13 of of IN 10_1101-2020_10_26_351783 11 14 19 19 CD 10_1101-2020_10_26_351783 11 15 datasets dataset NNS 10_1101-2020_10_26_351783 11 16 of of IN 10_1101-2020_10_26_351783 11 17 multiple multiple JJ 10_1101-2020_10_26_351783 11 18 sclerosis sclerosis NN 10_1101-2020_10_26_351783 11 19 ( ( -LRB- 10_1101-2020_10_26_351783 11 20 MS MS NNP 10_1101-2020_10_26_351783 11 21 ) ) -RRB- 10_1101-2020_10_26_351783 11 22 , , , 10_1101-2020_10_26_351783 11 23 and and CC 10_1101-2020_10_26_351783 11 24 further further RB 10_1101-2020_10_26_351783 11 25 validated validate VBD 10_1101-2020_10_26_351783 11 26 the the DT 10_1101-2020_10_26_351783 11 27 resulting result VBG 10_1101-2020_10_26_351783 11 28 module module NN 10_1101-2020_10_26_351783 11 29 using use VBG 10_1101-2020_10_26_351783 11 30 both both CC 10_1101-2020_10_26_351783 11 31 GWAS GWAS NNP 10_1101-2020_10_26_351783 11 32 and and CC 10_1101-2020_10_26_351783 11 33 risk risk NN 10_1101-2020_10_26_351783 11 34 - - HYPH 10_1101-2020_10_26_351783 11 35 factor factor NN 10_1101-2020_10_26_351783 11 36 associated associate VBN 10_1101-2020_10_26_351783 11 37 genes gene NNS 10_1101-2020_10_26_351783 11 38 from from IN 10_1101-2020_10_26_351783 11 39 several several JJ 10_1101-2020_10_26_351783 11 40 independent independent JJ 10_1101-2020_10_26_351783 11 41 cohorts cohort NNS 10_1101-2020_10_26_351783 11 42 . . . 10_1101-2020_10_26_351783 12 1 Results result NNS 10_1101-2020_10_26_351783 12 2 : : : 10_1101-2020_10_26_351783 12 3 Our -PRON- PRP$ 10_1101-2020_10_26_351783 12 4 benchmark benchmark NN 10_1101-2020_10_26_351783 12 5 of of IN 10_1101-2020_10_26_351783 12 6 modules module NNS 10_1101-2020_10_26_351783 12 7 showed show VBD 10_1101-2020_10_26_351783 12 8 that that IN 10_1101-2020_10_26_351783 12 9 in in IN 10_1101-2020_10_26_351783 12 10 immune immune NN 10_1101-2020_10_26_351783 12 11 - - HYPH 10_1101-2020_10_26_351783 12 12 associated associate VBN 10_1101-2020_10_26_351783 12 13 diseases disease NNS 10_1101-2020_10_26_351783 12 14 modules module NNS 10_1101-2020_10_26_351783 12 15 inferred infer VBN 10_1101-2020_10_26_351783 12 16 from from IN 10_1101-2020_10_26_351783 12 17 clique clique NN 10_1101-2020_10_26_351783 12 18 - - HYPH 10_1101-2020_10_26_351783 12 19 based base VBN 10_1101-2020_10_26_351783 12 20 methods method NNS 10_1101-2020_10_26_351783 12 21 were be VBD 10_1101-2020_10_26_351783 12 22 the the DT 10_1101-2020_10_26_351783 12 23 most most RBS 10_1101-2020_10_26_351783 12 24 enriched enrich VBN 10_1101-2020_10_26_351783 12 25 for for IN 10_1101-2020_10_26_351783 12 26 GWAS gwas NN 10_1101-2020_10_26_351783 12 27 - - HYPH 10_1101-2020_10_26_351783 12 28 genes gene NNS 10_1101-2020_10_26_351783 12 29 . . . 10_1101-2020_10_26_351783 13 1 The the DT 10_1101-2020_10_26_351783 13 2 multi multi JJ 10_1101-2020_10_26_351783 13 3 - - HYPH 10_1101-2020_10_26_351783 13 4 omics omic NNS 10_1101-2020_10_26_351783 13 5 case case NN 10_1101-2020_10_26_351783 13 6 study study NN 10_1101-2020_10_26_351783 13 7 using use VBG 10_1101-2020_10_26_351783 13 8 MS MS NNP 10_1101-2020_10_26_351783 13 9 revealed reveal VBD 10_1101-2020_10_26_351783 13 10 the the DT 10_1101-2020_10_26_351783 13 11 robust robust JJ 10_1101-2020_10_26_351783 13 12 identification identification NN 10_1101-2020_10_26_351783 13 13 of of IN 10_1101-2020_10_26_351783 13 14 a a DT 10_1101-2020_10_26_351783 13 15 module module NN 10_1101-2020_10_26_351783 13 16 of of IN 10_1101-2020_10_26_351783 13 17 220 220 CD 10_1101-2020_10_26_351783 13 18 genes gene NNS 10_1101-2020_10_26_351783 13 19 . . . 10_1101-2020_10_26_351783 14 1 Strikingly strikingly RB 10_1101-2020_10_26_351783 14 2 , , , 10_1101-2020_10_26_351783 14 3 most most JJS 10_1101-2020_10_26_351783 14 4 genes gene NNS 10_1101-2020_10_26_351783 14 5 of of IN 10_1101-2020_10_26_351783 14 6 the the DT 10_1101-2020_10_26_351783 14 7 module module NN 10_1101-2020_10_26_351783 14 8 was be VBD 10_1101-2020_10_26_351783 14 9 differentially differentially RB 10_1101-2020_10_26_351783 14 10 methylated methylate VBN 10_1101-2020_10_26_351783 14 11 upon upon IN 10_1101-2020_10_26_351783 14 12 the the DT 10_1101-2020_10_26_351783 14 13 action action NN 10_1101-2020_10_26_351783 14 14 of of IN 10_1101-2020_10_26_351783 14 15 one one CD 10_1101-2020_10_26_351783 14 16 or or CC 10_1101-2020_10_26_351783 14 17 several several JJ 10_1101-2020_10_26_351783 14 18 environmental environmental JJ 10_1101-2020_10_26_351783 14 19 risk risk NN 10_1101-2020_10_26_351783 14 20 factors factor NNS 10_1101-2020_10_26_351783 14 21 in in IN 10_1101-2020_10_26_351783 14 22 MS MS NNP 10_1101-2020_10_26_351783 14 23 ( ( -LRB- 10_1101-2020_10_26_351783 14 24 n n NNP 10_1101-2020_10_26_351783 14 25 = = SYM 10_1101-2020_10_26_351783 14 26 217 217 CD 10_1101-2020_10_26_351783 14 27 , , , 10_1101-2020_10_26_351783 14 28 P p NN 10_1101-2020_10_26_351783 14 29 = = SYM 10_1101-2020_10_26_351783 14 30 10 10 CD 10_1101-2020_10_26_351783 14 31 - - SYM 10_1101-2020_10_26_351783 14 32 47 47 CD 10_1101-2020_10_26_351783 14 33 ) ) -RRB- 10_1101-2020_10_26_351783 14 34 and and CC 10_1101-2020_10_26_351783 14 35 were be VBD 10_1101-2020_10_26_351783 14 36 also also RB 10_1101-2020_10_26_351783 14 37 independently independently RB 10_1101-2020_10_26_351783 14 38 validated validate VBN 10_1101-2020_10_26_351783 14 39 for for IN 10_1101-2020_10_26_351783 14 40 association association NN 10_1101-2020_10_26_351783 14 41 with with IN 10_1101-2020_10_26_351783 14 42 five five CD 10_1101-2020_10_26_351783 14 43 different different JJ 10_1101-2020_10_26_351783 14 44 risk risk NN 10_1101-2020_10_26_351783 14 45 factors factor NNS 10_1101-2020_10_26_351783 14 46 of of IN 10_1101-2020_10_26_351783 14 47 MS MS NNP 10_1101-2020_10_26_351783 14 48 , , , 10_1101-2020_10_26_351783 14 49 which which WDT 10_1101-2020_10_26_351783 14 50 further further RB 10_1101-2020_10_26_351783 14 51 stressed stress VBD 10_1101-2020_10_26_351783 14 52 the the DT 10_1101-2020_10_26_351783 14 53 high high JJ 10_1101-2020_10_26_351783 14 54 genetic genetic JJ 10_1101-2020_10_26_351783 14 55 and and CC 10_1101-2020_10_26_351783 14 56 epigenetic epigenetic JJ 10_1101-2020_10_26_351783 14 57 relevance relevance NN 10_1101-2020_10_26_351783 14 58 of of IN 10_1101-2020_10_26_351783 14 59 the the DT 10_1101-2020_10_26_351783 14 60 module module NN 10_1101-2020_10_26_351783 14 61 for for IN 10_1101-2020_10_26_351783 14 62 MS MS NNP 10_1101-2020_10_26_351783 14 63 . . . 10_1101-2020_10_26_351783 15 1 Conclusion conclusion NN 10_1101-2020_10_26_351783 15 2 : : : 10_1101-2020_10_26_351783 15 3 We -PRON- PRP 10_1101-2020_10_26_351783 15 4 believe believe VBP 10_1101-2020_10_26_351783 15 5 our -PRON- PRP$ 10_1101-2020_10_26_351783 15 6 analysis analysis NN 10_1101-2020_10_26_351783 15 7 provides provide VBZ 10_1101-2020_10_26_351783 15 8 a a DT 10_1101-2020_10_26_351783 15 9 workflow workflow NN 10_1101-2020_10_26_351783 15 10 for for IN 10_1101-2020_10_26_351783 15 11 selecting select VBG 10_1101-2020_10_26_351783 15 12 modules module NNS 10_1101-2020_10_26_351783 15 13 and and CC 10_1101-2020_10_26_351783 15 14 our -PRON- PRP$ 10_1101-2020_10_26_351783 15 15 benchmark benchmark JJ 10_1101-2020_10_26_351783 15 16 study study NN 10_1101-2020_10_26_351783 15 17 may may MD 10_1101-2020_10_26_351783 15 18 help help VB 10_1101-2020_10_26_351783 15 19 further further JJ 10_1101-2020_10_26_351783 15 20 improvement improvement NN 10_1101-2020_10_26_351783 15 21 of of IN 10_1101-2020_10_26_351783 15 22 disease disease NN 10_1101-2020_10_26_351783 15 23 module module NN 10_1101-2020_10_26_351783 15 24 methods method NNS 10_1101-2020_10_26_351783 15 25 . . . 10_1101-2020_10_26_351783 16 1 Moreover moreover RB 10_1101-2020_10_26_351783 16 2 , , , 10_1101-2020_10_26_351783 16 3 we -PRON- PRP 10_1101-2020_10_26_351783 16 4 also also RB 10_1101-2020_10_26_351783 16 5 stress stress VBP 10_1101-2020_10_26_351783 16 6 that that IN 10_1101-2020_10_26_351783 16 7 our -PRON- PRP$ 10_1101-2020_10_26_351783 16 8 methodology methodology NN 10_1101-2020_10_26_351783 16 9 is be VBZ 10_1101-2020_10_26_351783 16 10 generally generally RB 10_1101-2020_10_26_351783 16 11 applicable applicable JJ 10_1101-2020_10_26_351783 16 12 for for IN 10_1101-2020_10_26_351783 16 13 combining combine VBG 10_1101-2020_10_26_351783 16 14 and and CC 10_1101-2020_10_26_351783 16 15 assessing assess VBG 10_1101-2020_10_26_351783 16 16 the the DT 10_1101-2020_10_26_351783 16 17 performance performance NN 10_1101-2020_10_26_351783 16 18 of of IN 10_1101-2020_10_26_351783 16 19 multi multi JJ 10_1101-2020_10_26_351783 16 20 - - JJ 10_1101-2020_10_26_351783 16 21 omics omics JJ 10_1101-2020_10_26_351783 16 22 approaches approach NNS 10_1101-2020_10_26_351783 16 23 for for IN 10_1101-2020_10_26_351783 16 24 complex complex JJ 10_1101-2020_10_26_351783 16 25 diseases disease NNS 10_1101-2020_10_26_351783 16 26 . . . 10_1101-2020_10_26_351783 17 1 ( ( -LRB- 10_1101-2020_10_26_351783 17 2 which which WDT 10_1101-2020_10_26_351783 17 3 was be VBD 10_1101-2020_10_26_351783 17 4 not not RB 10_1101-2020_10_26_351783 17 5 certified certify VBN 10_1101-2020_10_26_351783 17 6 by by IN 10_1101-2020_10_26_351783 17 7 peer peer NN 10_1101-2020_10_26_351783 17 8 review review NN 10_1101-2020_10_26_351783 17 9 ) ) -RRB- 10_1101-2020_10_26_351783 17 10 is be VBZ 10_1101-2020_10_26_351783 17 11 the the DT 10_1101-2020_10_26_351783 17 12 author author NN 10_1101-2020_10_26_351783 17 13 / / SYM 10_1101-2020_10_26_351783 17 14 funder funder NN 10_1101-2020_10_26_351783 17 15 . . . 10_1101-2020_10_26_351783 18 1 All all DT 10_1101-2020_10_26_351783 18 2 rights right NNS 10_1101-2020_10_26_351783 18 3 reserved reserve VBD 10_1101-2020_10_26_351783 18 4 . . . 10_1101-2020_10_26_351783 19 1 No no DT 10_1101-2020_10_26_351783 19 2 reuse reuse NN 10_1101-2020_10_26_351783 19 3 allowed allow VBN 10_1101-2020_10_26_351783 19 4 without without IN 10_1101-2020_10_26_351783 19 5 permission permission NN 10_1101-2020_10_26_351783 19 6 . . . 10_1101-2020_10_26_351783 20 1 The the DT 10_1101-2020_10_26_351783 20 2 copyright copyright NN 10_1101-2020_10_26_351783 20 3 holder holder NN 10_1101-2020_10_26_351783 20 4 for for IN 10_1101-2020_10_26_351783 20 5 this this DT 10_1101-2020_10_26_351783 20 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 20 7 version version NN 10_1101-2020_10_26_351783 20 8 posted post VBD 10_1101-2020_10_26_351783 20 9 January January NNP 10_1101-2020_10_26_351783 20 10 6 6 CD 10_1101-2020_10_26_351783 20 11 , , , 10_1101-2020_10_26_351783 20 12 2021 2021 CD 10_1101-2020_10_26_351783 20 13 . . . 10_1101-2020_10_26_351783 20 14 ; ; : 10_1101-2020_10_26_351783 20 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 20 16 : : : 10_1101-2020_10_26_351783 20 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 20 18 preprint preprint NN 10_1101-2020_10_26_351783 20 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 20 20 3 3 CD 10_1101-2020_10_26_351783 20 21 INTRODUCTION introduction NN 10_1101-2020_10_26_351783 20 22 Complex complex JJ 10_1101-2020_10_26_351783 20 23 diseases disease NNS 10_1101-2020_10_26_351783 20 24 are be VBP 10_1101-2020_10_26_351783 20 25 the the DT 10_1101-2020_10_26_351783 20 26 result result NN 10_1101-2020_10_26_351783 20 27 of of IN 10_1101-2020_10_26_351783 20 28 disruptions disruption NNS 10_1101-2020_10_26_351783 20 29 of of IN 10_1101-2020_10_26_351783 20 30 many many JJ 10_1101-2020_10_26_351783 20 31 interconnected interconnected JJ 10_1101-2020_10_26_351783 20 32 multimolecular multimolecular JJ 10_1101-2020_10_26_351783 20 33 pathways pathway NNS 10_1101-2020_10_26_351783 20 34 , , , 10_1101-2020_10_26_351783 20 35 reflected reflect VBN 10_1101-2020_10_26_351783 20 36 in in IN 10_1101-2020_10_26_351783 20 37 multiple multiple JJ 10_1101-2020_10_26_351783 20 38 omics omic NNS 10_1101-2020_10_26_351783 20 39 layers layer NNS 10_1101-2020_10_26_351783 20 40 of of IN 10_1101-2020_10_26_351783 20 41 regulation regulation NN 10_1101-2020_10_26_351783 20 42 of of IN 10_1101-2020_10_26_351783 20 43 cellular cellular JJ 10_1101-2020_10_26_351783 20 44 function function NN 10_1101-2020_10_26_351783 20 45 , , , 10_1101-2020_10_26_351783 20 46 rather rather RB 10_1101-2020_10_26_351783 20 47 than than IN 10_1101-2020_10_26_351783 20 48 perturbations perturbation NNS 10_1101-2020_10_26_351783 20 49 of of IN 10_1101-2020_10_26_351783 20 50 a a DT 10_1101-2020_10_26_351783 20 51 single single JJ 10_1101-2020_10_26_351783 20 52 gene gene NN 10_1101-2020_10_26_351783 20 53 or or CC 10_1101-2020_10_26_351783 20 54 protein[1 protein[1 NNP 10_1101-2020_10_26_351783 20 55 ] ] -RRB- 10_1101-2020_10_26_351783 20 56 . . . 10_1101-2020_10_26_351783 21 1 Systems system NNS 10_1101-2020_10_26_351783 21 2 and and CC 10_1101-2020_10_26_351783 21 3 network network NN 10_1101-2020_10_26_351783 21 4 medicine medicine NN 10_1101-2020_10_26_351783 21 5 aim aim NN 10_1101-2020_10_26_351783 21 6 to to TO 10_1101-2020_10_26_351783 21 7 translate translate VB 10_1101-2020_10_26_351783 21 8 observed observed JJ 10_1101-2020_10_26_351783 21 9 omics omic NNS 10_1101-2020_10_26_351783 21 10 differences difference NNS 10_1101-2020_10_26_351783 21 11 in in IN 10_1101-2020_10_26_351783 21 12 patients patient NNS 10_1101-2020_10_26_351783 21 13 using use VBG 10_1101-2020_10_26_351783 21 14 networks network NNS 10_1101-2020_10_26_351783 21 15 , , , 10_1101-2020_10_26_351783 21 16 in in IN 10_1101-2020_10_26_351783 21 17 order order NN 10_1101-2020_10_26_351783 21 18 to to TO 10_1101-2020_10_26_351783 21 19 personalize personalize VB 10_1101-2020_10_26_351783 21 20 medicine[2 medicine[2 NNP 10_1101-2020_10_26_351783 21 21 ] ] -RRB- 10_1101-2020_10_26_351783 21 22 . . . 10_1101-2020_10_26_351783 22 1 Importantly importantly RB 10_1101-2020_10_26_351783 22 2 , , , 10_1101-2020_10_26_351783 22 3 genes gene NNS 10_1101-2020_10_26_351783 22 4 that that WDT 10_1101-2020_10_26_351783 22 5 are be VBP 10_1101-2020_10_26_351783 22 6 associated associate VBN 10_1101-2020_10_26_351783 22 7 with with IN 10_1101-2020_10_26_351783 22 8 diseases disease NNS 10_1101-2020_10_26_351783 22 9 are be VBP 10_1101-2020_10_26_351783 22 10 more more RBR 10_1101-2020_10_26_351783 22 11 likely likely JJ 10_1101-2020_10_26_351783 22 12 to to TO 10_1101-2020_10_26_351783 22 13 interact interact VB 10_1101-2020_10_26_351783 22 14 with with IN 10_1101-2020_10_26_351783 22 15 each each DT 10_1101-2020_10_26_351783 22 16 other other JJ 10_1101-2020_10_26_351783 22 17 rather rather RB 10_1101-2020_10_26_351783 22 18 than than IN 10_1101-2020_10_26_351783 22 19 with with IN 10_1101-2020_10_26_351783 22 20 non non JJ 10_1101-2020_10_26_351783 22 21 - - JJ 10_1101-2020_10_26_351783 22 22 disease disease JJ 10_1101-2020_10_26_351783 22 23 associated associate VBN 10_1101-2020_10_26_351783 22 24 genes gene NNS 10_1101-2020_10_26_351783 22 25 , , , 10_1101-2020_10_26_351783 22 26 forming form VBG 10_1101-2020_10_26_351783 22 27 multi multi JJ 10_1101-2020_10_26_351783 22 28 - - NNS 10_1101-2020_10_26_351783 22 29 omics omic NNS 10_1101-2020_10_26_351783 22 30 network network NN 10_1101-2020_10_26_351783 22 31 disease disease NNP 10_1101-2020_10_26_351783 22 32 modules[3,4 modules[3,4 NNP 10_1101-2020_10_26_351783 22 33 ] ] -RRB- 10_1101-2020_10_26_351783 22 34 . . . 10_1101-2020_10_26_351783 23 1 Owing owe VBG 10_1101-2020_10_26_351783 23 2 to to IN 10_1101-2020_10_26_351783 23 3 the the DT 10_1101-2020_10_26_351783 23 4 incompleteness incompleteness NN 10_1101-2020_10_26_351783 23 5 of of IN 10_1101-2020_10_26_351783 23 6 the the DT 10_1101-2020_10_26_351783 23 7 underlying underlying JJ 10_1101-2020_10_26_351783 23 8 multi multi JJ 10_1101-2020_10_26_351783 23 9 - - HYPH 10_1101-2020_10_26_351783 23 10 omics omic NNS 10_1101-2020_10_26_351783 23 11 interactions interaction NNS 10_1101-2020_10_26_351783 23 12 , , , 10_1101-2020_10_26_351783 23 13 the the DT 10_1101-2020_10_26_351783 23 14 networks network NNS 10_1101-2020_10_26_351783 23 15 are be VBP 10_1101-2020_10_26_351783 23 16 often often RB 10_1101-2020_10_26_351783 23 17 modeled model VBN 10_1101-2020_10_26_351783 23 18 as as IN 10_1101-2020_10_26_351783 23 19 effective effective JJ 10_1101-2020_10_26_351783 23 20 gene gene NN 10_1101-2020_10_26_351783 23 21 - - HYPH 10_1101-2020_10_26_351783 23 22 gene gene NN 10_1101-2020_10_26_351783 23 23 interactions interaction NNS 10_1101-2020_10_26_351783 23 24 , , , 10_1101-2020_10_26_351783 23 25 using use VBG 10_1101-2020_10_26_351783 23 26 for for IN 10_1101-2020_10_26_351783 23 27 example example NN 10_1101-2020_10_26_351783 23 28 STRING STRING NNP 10_1101-2020_10_26_351783 23 29 database[5 database[5 NNP 10_1101-2020_10_26_351783 23 30 ] ] -RRB- 10_1101-2020_10_26_351783 23 31 . . . 10_1101-2020_10_26_351783 24 1 Thus thus RB 10_1101-2020_10_26_351783 24 2 , , , 10_1101-2020_10_26_351783 24 3 network network NN 10_1101-2020_10_26_351783 24 4 modules module NNS 10_1101-2020_10_26_351783 24 5 might may MD 10_1101-2020_10_26_351783 24 6 be be VB 10_1101-2020_10_26_351783 24 7 ideal ideal JJ 10_1101-2020_10_26_351783 24 8 tools tool NNS 10_1101-2020_10_26_351783 24 9 for for IN 10_1101-2020_10_26_351783 24 10 multi multi JJ 10_1101-2020_10_26_351783 24 11 - - NNS 10_1101-2020_10_26_351783 24 12 omics omic NNS 10_1101-2020_10_26_351783 24 13 analysis analysis NN 10_1101-2020_10_26_351783 24 14 . . . 10_1101-2020_10_26_351783 25 1 However however RB 10_1101-2020_10_26_351783 25 2 , , , 10_1101-2020_10_26_351783 25 3 the the DT 10_1101-2020_10_26_351783 25 4 evaluation evaluation NN 10_1101-2020_10_26_351783 25 5 of of IN 10_1101-2020_10_26_351783 25 6 performance performance NN 10_1101-2020_10_26_351783 25 7 of of IN 10_1101-2020_10_26_351783 25 8 different different JJ 10_1101-2020_10_26_351783 25 9 module module JJ 10_1101-2020_10_26_351783 25 10 inference inference NN 10_1101-2020_10_26_351783 25 11 methods method NNS 10_1101-2020_10_26_351783 25 12 remains remain VBZ 10_1101-2020_10_26_351783 25 13 a a DT 10_1101-2020_10_26_351783 25 14 poorly poorly RB 10_1101-2020_10_26_351783 25 15 understood understand VBN 10_1101-2020_10_26_351783 25 16 topic topic NN 10_1101-2020_10_26_351783 25 17 , , , 10_1101-2020_10_26_351783 25 18 which which WDT 10_1101-2020_10_26_351783 25 19 creates create VBZ 10_1101-2020_10_26_351783 25 20 the the DT 10_1101-2020_10_26_351783 25 21 need need NN 10_1101-2020_10_26_351783 25 22 for for IN 10_1101-2020_10_26_351783 25 23 transparent transparent JJ 10_1101-2020_10_26_351783 25 24 evaluation evaluation NN 10_1101-2020_10_26_351783 25 25 of of IN 10_1101-2020_10_26_351783 25 26 these these DT 10_1101-2020_10_26_351783 25 27 methods method NNS 10_1101-2020_10_26_351783 25 28 based base VBN 10_1101-2020_10_26_351783 25 29 on on IN 10_1101-2020_10_26_351783 25 30 objective objective JJ 10_1101-2020_10_26_351783 25 31 benchmarks benchmark NNS 10_1101-2020_10_26_351783 25 32 across across IN 10_1101-2020_10_26_351783 25 33 various various JJ 10_1101-2020_10_26_351783 25 34 diseases disease NNS 10_1101-2020_10_26_351783 25 35 and and CC 10_1101-2020_10_26_351783 25 36 omics omic NNS 10_1101-2020_10_26_351783 25 37 . . . 10_1101-2020_10_26_351783 26 1 Genomic genomic JJ 10_1101-2020_10_26_351783 26 2 concordance concordance NN 10_1101-2020_10_26_351783 26 3 has have VBZ 10_1101-2020_10_26_351783 26 4 been be VBN 10_1101-2020_10_26_351783 26 5 suggested suggest VBN 10_1101-2020_10_26_351783 26 6 as as IN 10_1101-2020_10_26_351783 26 7 a a DT 10_1101-2020_10_26_351783 26 8 multi multi JJ 10_1101-2020_10_26_351783 26 9 - - HYPH 10_1101-2020_10_26_351783 26 10 omics omic NNS 10_1101-2020_10_26_351783 26 11 validation validation NN 10_1101-2020_10_26_351783 26 12 principle[4,6 principle[4,6 NNP 10_1101-2020_10_26_351783 26 13 ] ] -RRB- 10_1101-2020_10_26_351783 26 14 , , , 10_1101-2020_10_26_351783 26 15 i.e. i.e. FW 10_1101-2020_10_26_351783 26 16 , , , 10_1101-2020_10_26_351783 26 17 modules module NNS 10_1101-2020_10_26_351783 26 18 derived derive VBN 10_1101-2020_10_26_351783 26 19 from from IN 10_1101-2020_10_26_351783 26 20 one one CD 10_1101-2020_10_26_351783 26 21 omic omic JJ 10_1101-2020_10_26_351783 26 22 , , , 10_1101-2020_10_26_351783 26 23 such such JJ 10_1101-2020_10_26_351783 26 24 as as IN 10_1101-2020_10_26_351783 26 25 gene gene NN 10_1101-2020_10_26_351783 26 26 expression expression NN 10_1101-2020_10_26_351783 26 27 or or CC 10_1101-2020_10_26_351783 26 28 DNA dna NN 10_1101-2020_10_26_351783 26 29 methylation methylation NN 10_1101-2020_10_26_351783 26 30 should should MD 10_1101-2020_10_26_351783 26 31 be be VB 10_1101-2020_10_26_351783 26 32 enriched enrich VBN 10_1101-2020_10_26_351783 26 33 for for IN 10_1101-2020_10_26_351783 26 34 disease- disease- NNP 10_1101-2020_10_26_351783 26 35 associated associated NNP 10_1101-2020_10_26_351783 26 36 single single JJ 10_1101-2020_10_26_351783 26 37 nucleotide nucleotide JJ 10_1101-2020_10_26_351783 26 38 polymorphisms polymorphism NNS 10_1101-2020_10_26_351783 26 39 ( ( -LRB- 10_1101-2020_10_26_351783 26 40 SNPs SNPs NNP 10_1101-2020_10_26_351783 26 41 ) ) -RRB- 10_1101-2020_10_26_351783 26 42 . . . 10_1101-2020_10_26_351783 27 1 The the DT 10_1101-2020_10_26_351783 27 2 variety variety NN 10_1101-2020_10_26_351783 27 3 of of IN 10_1101-2020_10_26_351783 27 4 algorithms algorithm NNS 10_1101-2020_10_26_351783 27 5 that that WDT 10_1101-2020_10_26_351783 27 6 have have VBP 10_1101-2020_10_26_351783 27 7 been be VBN 10_1101-2020_10_26_351783 27 8 proposed propose VBN 10_1101-2020_10_26_351783 27 9 and and CC 10_1101-2020_10_26_351783 27 10 applied apply VBN 10_1101-2020_10_26_351783 27 11 for for IN 10_1101-2020_10_26_351783 27 12 identification identification NN 10_1101-2020_10_26_351783 27 13 of of IN 10_1101-2020_10_26_351783 27 14 disease disease NN 10_1101-2020_10_26_351783 27 15 modules module NNS 10_1101-2020_10_26_351783 27 16 can can MD 10_1101-2020_10_26_351783 27 17 be be VB 10_1101-2020_10_26_351783 27 18 categorized categorize VBN 10_1101-2020_10_26_351783 27 19 into into IN 10_1101-2020_10_26_351783 27 20 two two CD 10_1101-2020_10_26_351783 27 21 main main JJ 10_1101-2020_10_26_351783 27 22 groups group NNS 10_1101-2020_10_26_351783 27 23 . . . 10_1101-2020_10_26_351783 28 1 On on IN 10_1101-2020_10_26_351783 28 2 the the DT 10_1101-2020_10_26_351783 28 3 one one CD 10_1101-2020_10_26_351783 28 4 hand hand NN 10_1101-2020_10_26_351783 28 5 , , , 10_1101-2020_10_26_351783 28 6 there there EX 10_1101-2020_10_26_351783 28 7 are be VBP 10_1101-2020_10_26_351783 28 8 methods method NNS 10_1101-2020_10_26_351783 28 9 which which WDT 10_1101-2020_10_26_351783 28 10 rely rely VBP 10_1101-2020_10_26_351783 28 11 purely purely RB 10_1101-2020_10_26_351783 28 12 on on IN 10_1101-2020_10_26_351783 28 13 clustering clustering NN 10_1101-2020_10_26_351783 28 14 of of IN 10_1101-2020_10_26_351783 28 15 the the DT 10_1101-2020_10_26_351783 28 16 genes gene NNS 10_1101-2020_10_26_351783 28 17 in in IN 10_1101-2020_10_26_351783 28 18 relevant relevant JJ 10_1101-2020_10_26_351783 28 19 disease disease NN 10_1101-2020_10_26_351783 28 20 networks[7 networks[7 NNP 10_1101-2020_10_26_351783 28 21 ] ] -RRB- 10_1101-2020_10_26_351783 28 22 . . . 10_1101-2020_10_26_351783 29 1 On on IN 10_1101-2020_10_26_351783 29 2 the the DT 10_1101-2020_10_26_351783 29 3 other other JJ 10_1101-2020_10_26_351783 29 4 hand hand NN 10_1101-2020_10_26_351783 29 5 , , , 10_1101-2020_10_26_351783 29 6 there there EX 10_1101-2020_10_26_351783 29 7 are be VBP 10_1101-2020_10_26_351783 29 8 algorithms algorithm NNS 10_1101-2020_10_26_351783 29 9 which which WDT 10_1101-2020_10_26_351783 29 10 make make VBP 10_1101-2020_10_26_351783 29 11 use use NN 10_1101-2020_10_26_351783 29 12 of of IN 10_1101-2020_10_26_351783 29 13 disease disease NN 10_1101-2020_10_26_351783 29 14 - - HYPH 10_1101-2020_10_26_351783 29 15 associated associate VBN 10_1101-2020_10_26_351783 29 16 molecules molecule NNS 10_1101-2020_10_26_351783 29 17 or or CC 10_1101-2020_10_26_351783 29 18 genetic genetic JJ 10_1101-2020_10_26_351783 29 19 loci loci NN 10_1101-2020_10_26_351783 29 20 to to TO 10_1101-2020_10_26_351783 29 21 reveal reveal VB 10_1101-2020_10_26_351783 29 22 disease disease NN 10_1101-2020_10_26_351783 29 23 modules module NNS 10_1101-2020_10_26_351783 29 24 that that WDT 10_1101-2020_10_26_351783 29 25 correlate correlate VBP 10_1101-2020_10_26_351783 29 26 with with IN 10_1101-2020_10_26_351783 29 27 disease disease NN 10_1101-2020_10_26_351783 29 28 function function NN 10_1101-2020_10_26_351783 29 29 , , , 10_1101-2020_10_26_351783 29 30 such such JJ 10_1101-2020_10_26_351783 29 31 as as IN 10_1101-2020_10_26_351783 29 32 the the DT 10_1101-2020_10_26_351783 29 33 disease disease NN 10_1101-2020_10_26_351783 29 34 module module NNP 10_1101-2020_10_26_351783 29 35 detection detection NN 10_1101-2020_10_26_351783 29 36 ( ( -LRB- 10_1101-2020_10_26_351783 29 37 DIAMOnD diamond NN 10_1101-2020_10_26_351783 29 38 ) ) -RRB- 10_1101-2020_10_26_351783 29 39 algorithm[8 algorithm[8 NNP 10_1101-2020_10_26_351783 29 40 ] ] -RRB- 10_1101-2020_10_26_351783 29 41 , , , 10_1101-2020_10_26_351783 29 42 clique clique NN 10_1101-2020_10_26_351783 29 43 - - HYPH 10_1101-2020_10_26_351783 29 44 based base VBN 10_1101-2020_10_26_351783 29 45 methods[9],[10 methods[9],[10 NNP 10_1101-2020_10_26_351783 29 46 ] ] -RRB- 10_1101-2020_10_26_351783 29 47 and and CC 10_1101-2020_10_26_351783 29 48 weighted weight VBD 10_1101-2020_10_26_351783 29 49 gene gene NN 10_1101-2020_10_26_351783 29 50 co co NN 10_1101-2020_10_26_351783 29 51 - - JJ 10_1101-2020_10_26_351783 29 52 expression expression JJ 10_1101-2020_10_26_351783 29 53 network network NN 10_1101-2020_10_26_351783 29 54 analysis analysis NN 10_1101-2020_10_26_351783 29 55 ( ( -LRB- 10_1101-2020_10_26_351783 29 56 WGCNA)[11 WGCNA)[11 NNP 10_1101-2020_10_26_351783 29 57 ] ] -RRB- 10_1101-2020_10_26_351783 29 58 . . . 10_1101-2020_10_26_351783 30 1 The the DT 10_1101-2020_10_26_351783 30 2 data data NN 10_1101-2020_10_26_351783 30 3 - - HYPH 10_1101-2020_10_26_351783 30 4 derived derive VBN 10_1101-2020_10_26_351783 30 5 information information NN 10_1101-2020_10_26_351783 30 6 can can MD 10_1101-2020_10_26_351783 30 7 either either CC 10_1101-2020_10_26_351783 30 8 be be VB 10_1101-2020_10_26_351783 30 9 differentially differentially RB 10_1101-2020_10_26_351783 30 10 expressed express VBN 10_1101-2020_10_26_351783 30 11 genes gene NNS 10_1101-2020_10_26_351783 30 12 or or CC 10_1101-2020_10_26_351783 30 13 differentially differentially RB 10_1101-2020_10_26_351783 30 14 correlated correlate VBN 10_1101-2020_10_26_351783 30 15 or or CC 10_1101-2020_10_26_351783 30 16 co co VBN 10_1101-2020_10_26_351783 30 17 - - VBN 10_1101-2020_10_26_351783 30 18 expressed expressed JJ 10_1101-2020_10_26_351783 30 19 genes gene NNS 10_1101-2020_10_26_351783 30 20 . . . 10_1101-2020_10_26_351783 31 1 Methods method NNS 10_1101-2020_10_26_351783 31 2 following follow VBG 10_1101-2020_10_26_351783 31 3 the the DT 10_1101-2020_10_26_351783 31 4 former former JJ 10_1101-2020_10_26_351783 31 5 approach approach NN 10_1101-2020_10_26_351783 31 6 were be VBD 10_1101-2020_10_26_351783 31 7 recently recently RB 10_1101-2020_10_26_351783 31 8 benchmarked benchmarke VBN 10_1101-2020_10_26_351783 31 9 by by IN 10_1101-2020_10_26_351783 31 10 a a DT 10_1101-2020_10_26_351783 31 11 metric metric JJ 10_1101-2020_10_26_351783 31 12 utilizing utilize VBG 10_1101-2020_10_26_351783 31 13 genomic genomic JJ 10_1101-2020_10_26_351783 31 14 concordance concordance NN 10_1101-2020_10_26_351783 31 15 within within IN 10_1101-2020_10_26_351783 31 16 the the DT 10_1101-2020_10_26_351783 31 17 DREAM dream NN 10_1101-2020_10_26_351783 31 18 consortia[12 consortia[12 NN 10_1101-2020_10_26_351783 31 19 ] ] -RRB- 10_1101-2020_10_26_351783 31 20 . . . 10_1101-2020_10_26_351783 32 1 However however RB 10_1101-2020_10_26_351783 32 2 , , , 10_1101-2020_10_26_351783 32 3 so so RB 10_1101-2020_10_26_351783 32 4 far far RB 10_1101-2020_10_26_351783 32 5 , , , 10_1101-2020_10_26_351783 32 6 algorithms algorithm NNS 10_1101-2020_10_26_351783 32 7 from from IN 10_1101-2020_10_26_351783 32 8 the the DT 10_1101-2020_10_26_351783 32 9 latter latter JJ 10_1101-2020_10_26_351783 32 10 group group NN 10_1101-2020_10_26_351783 32 11 have have VBP 10_1101-2020_10_26_351783 32 12 not not RB 10_1101-2020_10_26_351783 32 13 been be VBN 10_1101-2020_10_26_351783 32 14 benchmarked benchmarke VBN 10_1101-2020_10_26_351783 32 15 . . . 10_1101-2020_10_26_351783 33 1 ( ( -LRB- 10_1101-2020_10_26_351783 33 2 which which WDT 10_1101-2020_10_26_351783 33 3 was be VBD 10_1101-2020_10_26_351783 33 4 not not RB 10_1101-2020_10_26_351783 33 5 certified certify VBN 10_1101-2020_10_26_351783 33 6 by by IN 10_1101-2020_10_26_351783 33 7 peer peer NN 10_1101-2020_10_26_351783 33 8 review review NN 10_1101-2020_10_26_351783 33 9 ) ) -RRB- 10_1101-2020_10_26_351783 33 10 is be VBZ 10_1101-2020_10_26_351783 33 11 the the DT 10_1101-2020_10_26_351783 33 12 author author NN 10_1101-2020_10_26_351783 33 13 / / SYM 10_1101-2020_10_26_351783 33 14 funder funder NN 10_1101-2020_10_26_351783 33 15 . . . 10_1101-2020_10_26_351783 34 1 All all DT 10_1101-2020_10_26_351783 34 2 rights right NNS 10_1101-2020_10_26_351783 34 3 reserved reserve VBD 10_1101-2020_10_26_351783 34 4 . . . 10_1101-2020_10_26_351783 35 1 No no DT 10_1101-2020_10_26_351783 35 2 reuse reuse NN 10_1101-2020_10_26_351783 35 3 allowed allow VBN 10_1101-2020_10_26_351783 35 4 without without IN 10_1101-2020_10_26_351783 35 5 permission permission NN 10_1101-2020_10_26_351783 35 6 . . . 10_1101-2020_10_26_351783 36 1 The the DT 10_1101-2020_10_26_351783 36 2 copyright copyright NN 10_1101-2020_10_26_351783 36 3 holder holder NN 10_1101-2020_10_26_351783 36 4 for for IN 10_1101-2020_10_26_351783 36 5 this this DT 10_1101-2020_10_26_351783 36 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 36 7 version version NN 10_1101-2020_10_26_351783 36 8 posted post VBD 10_1101-2020_10_26_351783 36 9 January January NNP 10_1101-2020_10_26_351783 36 10 6 6 CD 10_1101-2020_10_26_351783 36 11 , , , 10_1101-2020_10_26_351783 36 12 2021 2021 CD 10_1101-2020_10_26_351783 36 13 . . . 10_1101-2020_10_26_351783 36 14 ; ; : 10_1101-2020_10_26_351783 36 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 36 16 : : : 10_1101-2020_10_26_351783 36 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 36 18 preprint preprint NN 10_1101-2020_10_26_351783 36 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 36 20 4 4 CD 10_1101-2020_10_26_351783 36 21 In in IN 10_1101-2020_10_26_351783 36 22 this this DT 10_1101-2020_10_26_351783 36 23 study study NN 10_1101-2020_10_26_351783 36 24 we -PRON- PRP 10_1101-2020_10_26_351783 36 25 analyzed analyze VBD 10_1101-2020_10_26_351783 36 26 , , , 10_1101-2020_10_26_351783 36 27 assessed assess VBN 10_1101-2020_10_26_351783 36 28 , , , 10_1101-2020_10_26_351783 36 29 and and CC 10_1101-2020_10_26_351783 36 30 compared compare VBD 10_1101-2020_10_26_351783 36 31 the the DT 10_1101-2020_10_26_351783 36 32 performance performance NN 10_1101-2020_10_26_351783 36 33 of of IN 10_1101-2020_10_26_351783 36 34 eight eight CD 10_1101-2020_10_26_351783 36 35 of of IN 10_1101-2020_10_26_351783 36 36 the the DT 10_1101-2020_10_26_351783 36 37 most most RBS 10_1101-2020_10_26_351783 36 38 popular popular JJ 10_1101-2020_10_26_351783 36 39 methods method NNS 10_1101-2020_10_26_351783 36 40 for for IN 10_1101-2020_10_26_351783 36 41 disease disease NNP 10_1101-2020_10_26_351783 36 42 module module NNP 10_1101-2020_10_26_351783 36 43 analysis analysis NN 10_1101-2020_10_26_351783 36 44 using use VBG 10_1101-2020_10_26_351783 36 45 the the DT 10_1101-2020_10_26_351783 36 46 R r NN 10_1101-2020_10_26_351783 36 47 package package NN 10_1101-2020_10_26_351783 36 48 MODifieR[13 MODifieR[13 NNS 10_1101-2020_10_26_351783 36 49 ] ] -RRB- 10_1101-2020_10_26_351783 36 50 on on IN 10_1101-2020_10_26_351783 36 51 19 19 CD 10_1101-2020_10_26_351783 36 52 different different JJ 10_1101-2020_10_26_351783 36 53 diseases disease NNS 10_1101-2020_10_26_351783 36 54 including include VBG 10_1101-2020_10_26_351783 36 55 47 47 CD 10_1101-2020_10_26_351783 36 56 expression expression NN 10_1101-2020_10_26_351783 36 57 and and CC 10_1101-2020_10_26_351783 36 58 ten ten CD 10_1101-2020_10_26_351783 36 59 methylation methylation NN 10_1101-2020_10_26_351783 36 60 datasets dataset NNS 10_1101-2020_10_26_351783 36 61 . . . 10_1101-2020_10_26_351783 37 1 We -PRON- PRP 10_1101-2020_10_26_351783 37 2 assessed assess VBD 10_1101-2020_10_26_351783 37 3 the the DT 10_1101-2020_10_26_351783 37 4 performance performance NN 10_1101-2020_10_26_351783 37 5 of of IN 10_1101-2020_10_26_351783 37 6 the the DT 10_1101-2020_10_26_351783 37 7 methods method NNS 10_1101-2020_10_26_351783 37 8 using use VBG 10_1101-2020_10_26_351783 37 9 genome genome NN 10_1101-2020_10_26_351783 37 10 - - HYPH 10_1101-2020_10_26_351783 37 11 wide wide JJ 10_1101-2020_10_26_351783 37 12 association association NN 10_1101-2020_10_26_351783 37 13 ( ( -LRB- 10_1101-2020_10_26_351783 37 14 GWAS GWAS NNP 10_1101-2020_10_26_351783 37 15 ) ) -RRB- 10_1101-2020_10_26_351783 37 16 enrichment enrichment NN 10_1101-2020_10_26_351783 37 17 analysis analysis NN 10_1101-2020_10_26_351783 37 18 from from IN 10_1101-2020_10_26_351783 37 19 the the DT 10_1101-2020_10_26_351783 37 20 summary summary NN 10_1101-2020_10_26_351783 37 21 statistics statistic NNS 10_1101-2020_10_26_351783 37 22 of of IN 10_1101-2020_10_26_351783 37 23 all all DT 10_1101-2020_10_26_351783 37 24 assayed assay VBN 10_1101-2020_10_26_351783 37 25 SNPs snp NNS 10_1101-2020_10_26_351783 37 26 similarly similarly RB 10_1101-2020_10_26_351783 37 27 as as IN 10_1101-2020_10_26_351783 37 28 in in IN 10_1101-2020_10_26_351783 37 29 DREAM[12 DREAM[12 '' 10_1101-2020_10_26_351783 37 30 ] ] -RRB- 10_1101-2020_10_26_351783 37 31 . . . 10_1101-2020_10_26_351783 38 1 The the DT 10_1101-2020_10_26_351783 38 2 resulting result VBG 10_1101-2020_10_26_351783 38 3 workflow workflow NN 10_1101-2020_10_26_351783 38 4 provided provide VBD 10_1101-2020_10_26_351783 38 5 a a DT 10_1101-2020_10_26_351783 38 6 systematic systematic JJ 10_1101-2020_10_26_351783 38 7 procedure procedure NN 10_1101-2020_10_26_351783 38 8 for for IN 10_1101-2020_10_26_351783 38 9 selecting select VBG 10_1101-2020_10_26_351783 38 10 the the DT 10_1101-2020_10_26_351783 38 11 best good JJS 10_1101-2020_10_26_351783 38 12 method method NN 10_1101-2020_10_26_351783 38 13 for for IN 10_1101-2020_10_26_351783 38 14 each each DT 10_1101-2020_10_26_351783 38 15 disease disease NN 10_1101-2020_10_26_351783 38 16 and and CC 10_1101-2020_10_26_351783 38 17 set set VBD 10_1101-2020_10_26_351783 38 18 the the DT 10_1101-2020_10_26_351783 38 19 stage stage NN 10_1101-2020_10_26_351783 38 20 for for IN 10_1101-2020_10_26_351783 38 21 method method NN 10_1101-2020_10_26_351783 38 22 development development NN 10_1101-2020_10_26_351783 38 23 in in IN 10_1101-2020_10_26_351783 38 24 the the DT 10_1101-2020_10_26_351783 38 25 disease disease NNP 10_1101-2020_10_26_351783 38 26 module module NNP 10_1101-2020_10_26_351783 38 27 area area NN 10_1101-2020_10_26_351783 38 28 . . . 10_1101-2020_10_26_351783 39 1 Moreover moreover RB 10_1101-2020_10_26_351783 39 2 , , , 10_1101-2020_10_26_351783 39 3 it -PRON- PRP 10_1101-2020_10_26_351783 39 4 allowed allow VBD 10_1101-2020_10_26_351783 39 5 the the DT 10_1101-2020_10_26_351783 39 6 predictive predictive JJ 10_1101-2020_10_26_351783 39 7 assessment assessment NN 10_1101-2020_10_26_351783 39 8 of of IN 10_1101-2020_10_26_351783 39 9 combining combine VBG 10_1101-2020_10_26_351783 39 10 multiple multiple JJ 10_1101-2020_10_26_351783 39 11 datasets dataset NNS 10_1101-2020_10_26_351783 39 12 across across IN 10_1101-2020_10_26_351783 39 13 several several JJ 10_1101-2020_10_26_351783 39 14 omics omic NNS 10_1101-2020_10_26_351783 39 15 using use VBG 10_1101-2020_10_26_351783 39 16 GWAS GWAS NNP 10_1101-2020_10_26_351783 39 17 , , , 10_1101-2020_10_26_351783 39 18 which which WDT 10_1101-2020_10_26_351783 39 19 we -PRON- PRP 10_1101-2020_10_26_351783 39 20 tested test VBD 10_1101-2020_10_26_351783 39 21 in in IN 10_1101-2020_10_26_351783 39 22 multiple multiple JJ 10_1101-2020_10_26_351783 39 23 sclerosis sclerosis NN 10_1101-2020_10_26_351783 39 24 ( ( -LRB- 10_1101-2020_10_26_351783 39 25 MS MS NNP 10_1101-2020_10_26_351783 39 26 ) ) -RRB- 10_1101-2020_10_26_351783 39 27 , , , 10_1101-2020_10_26_351783 39 28 a a DT 10_1101-2020_10_26_351783 39 29 heterogeneous heterogeneous JJ 10_1101-2020_10_26_351783 39 30 complex complex JJ 10_1101-2020_10_26_351783 39 31 disease disease NN 10_1101-2020_10_26_351783 39 32 . . . 10_1101-2020_10_26_351783 40 1 Briefly briefly RB 10_1101-2020_10_26_351783 40 2 , , , 10_1101-2020_10_26_351783 40 3 we -PRON- PRP 10_1101-2020_10_26_351783 40 4 derived derive VBD 10_1101-2020_10_26_351783 40 5 multi multi JJ 10_1101-2020_10_26_351783 40 6 - - JJ 10_1101-2020_10_26_351783 40 7 omic omic JJ 10_1101-2020_10_26_351783 40 8 modules module NNS 10_1101-2020_10_26_351783 40 9 in in IN 10_1101-2020_10_26_351783 40 10 a a DT 10_1101-2020_10_26_351783 40 11 stepwise stepwise JJ 10_1101-2020_10_26_351783 40 12 optimization optimization NN 10_1101-2020_10_26_351783 40 13 of of IN 10_1101-2020_10_26_351783 40 14 GWAS GWAS NNP 10_1101-2020_10_26_351783 40 15 enrichment enrichment NN 10_1101-2020_10_26_351783 40 16 from from IN 10_1101-2020_10_26_351783 40 17 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 40 18 and and CC 10_1101-2020_10_26_351783 40 19 methylomic methylomic JJ 10_1101-2020_10_26_351783 40 20 analyses analysis NNS 10_1101-2020_10_26_351783 40 21 of of IN 10_1101-2020_10_26_351783 40 22 MS MS NNP 10_1101-2020_10_26_351783 40 23 . . . 10_1101-2020_10_26_351783 40 24 We -PRON- PRP 10_1101-2020_10_26_351783 40 25 further further RB 10_1101-2020_10_26_351783 40 26 evaluated evaluate VBD 10_1101-2020_10_26_351783 40 27 the the DT 10_1101-2020_10_26_351783 40 28 identified identify VBN 10_1101-2020_10_26_351783 40 29 multi multi JJ 10_1101-2020_10_26_351783 40 30 - - JJ 10_1101-2020_10_26_351783 40 31 omic omic JJ 10_1101-2020_10_26_351783 40 32 MS MS NNP 10_1101-2020_10_26_351783 40 33 module module NN 10_1101-2020_10_26_351783 40 34 of of IN 10_1101-2020_10_26_351783 40 35 220 220 CD 10_1101-2020_10_26_351783 40 36 genes gene NNS 10_1101-2020_10_26_351783 40 37 for for IN 10_1101-2020_10_26_351783 40 38 its -PRON- PRP$ 10_1101-2020_10_26_351783 40 39 enrichment enrichment NN 10_1101-2020_10_26_351783 40 40 across across IN 10_1101-2020_10_26_351783 40 41 DNA dna NN 10_1101-2020_10_26_351783 40 42 methylation methylation NN 10_1101-2020_10_26_351783 40 43 studies study NNS 10_1101-2020_10_26_351783 40 44 of of IN 10_1101-2020_10_26_351783 40 45 eight eight CD 10_1101-2020_10_26_351783 40 46 known know VBN 10_1101-2020_10_26_351783 40 47 lifestyle lifestyle NN 10_1101-2020_10_26_351783 40 48 - - HYPH 10_1101-2020_10_26_351783 40 49 associated associate VBN 10_1101-2020_10_26_351783 40 50 risk risk NN 10_1101-2020_10_26_351783 40 51 factors factor NNS 10_1101-2020_10_26_351783 40 52 of of IN 10_1101-2020_10_26_351783 40 53 MS MS NNP 10_1101-2020_10_26_351783 40 54 . . . 10_1101-2020_10_26_351783 40 55 Additionally additionally RB 10_1101-2020_10_26_351783 40 56 , , , 10_1101-2020_10_26_351783 40 57 we -PRON- PRP 10_1101-2020_10_26_351783 40 58 validated validate VBD 10_1101-2020_10_26_351783 40 59 the the DT 10_1101-2020_10_26_351783 40 60 identified identify VBN 10_1101-2020_10_26_351783 40 61 significant significant JJ 10_1101-2020_10_26_351783 40 62 enrichment enrichment NN 10_1101-2020_10_26_351783 40 63 risk risk NN 10_1101-2020_10_26_351783 40 64 factors factor NNS 10_1101-2020_10_26_351783 40 65 in in IN 10_1101-2020_10_26_351783 40 66 an an DT 10_1101-2020_10_26_351783 40 67 independent independent JJ 10_1101-2020_10_26_351783 40 68 DNA DNA NNP 10_1101-2020_10_26_351783 40 69 methylation methylation NN 10_1101-2020_10_26_351783 40 70 MS MS NNP 10_1101-2020_10_26_351783 40 71 study study NN 10_1101-2020_10_26_351783 40 72 which which WDT 10_1101-2020_10_26_351783 40 73 indeed indeed RB 10_1101-2020_10_26_351783 40 74 showed show VBD 10_1101-2020_10_26_351783 40 75 a a DT 10_1101-2020_10_26_351783 40 76 very very RB 10_1101-2020_10_26_351783 40 77 strong strong JJ 10_1101-2020_10_26_351783 40 78 and and CC 10_1101-2020_10_26_351783 40 79 significant significant JJ 10_1101-2020_10_26_351783 40 80 MS MS NNP 10_1101-2020_10_26_351783 40 81 enrichment enrichment NN 10_1101-2020_10_26_351783 40 82 for for IN 10_1101-2020_10_26_351783 40 83 both both DT 10_1101-2020_10_26_351783 40 84 module module JJ 10_1101-2020_10_26_351783 40 85 genes gene NNS 10_1101-2020_10_26_351783 40 86 and and CC 10_1101-2020_10_26_351783 40 87 risk risk NN 10_1101-2020_10_26_351783 40 88 factor factor NN 10_1101-2020_10_26_351783 40 89 associations association NNS 10_1101-2020_10_26_351783 40 90 . . . 10_1101-2020_10_26_351783 41 1 In in IN 10_1101-2020_10_26_351783 41 2 summary summary NN 10_1101-2020_10_26_351783 41 3 , , , 10_1101-2020_10_26_351783 41 4 we -PRON- PRP 10_1101-2020_10_26_351783 41 5 provide provide VBP 10_1101-2020_10_26_351783 41 6 a a DT 10_1101-2020_10_26_351783 41 7 robust robust JJ 10_1101-2020_10_26_351783 41 8 multi multi JJ 10_1101-2020_10_26_351783 41 9 - - HYPH 10_1101-2020_10_26_351783 41 10 omics omic NNS 10_1101-2020_10_26_351783 41 11 strategy strategy NN 10_1101-2020_10_26_351783 41 12 that that WDT 10_1101-2020_10_26_351783 41 13 can can MD 10_1101-2020_10_26_351783 41 14 be be VB 10_1101-2020_10_26_351783 41 15 used use VBN 10_1101-2020_10_26_351783 41 16 to to TO 10_1101-2020_10_26_351783 41 17 disentangle disentangle VB 10_1101-2020_10_26_351783 41 18 networks network NNS 10_1101-2020_10_26_351783 41 19 of of IN 10_1101-2020_10_26_351783 41 20 affected affect VBN 10_1101-2020_10_26_351783 41 21 genes gene NNS 10_1101-2020_10_26_351783 41 22 in in IN 10_1101-2020_10_26_351783 41 23 complex complex JJ 10_1101-2020_10_26_351783 41 24 diseases disease NNS 10_1101-2020_10_26_351783 41 25 from from IN 10_1101-2020_10_26_351783 41 26 both both CC 10_1101-2020_10_26_351783 41 27 genetic genetic JJ 10_1101-2020_10_26_351783 41 28 and and CC 10_1101-2020_10_26_351783 41 29 environmental environmental JJ 10_1101-2020_10_26_351783 41 30 levels level NNS 10_1101-2020_10_26_351783 41 31 . . . 10_1101-2020_10_26_351783 42 1 ( ( -LRB- 10_1101-2020_10_26_351783 42 2 which which WDT 10_1101-2020_10_26_351783 42 3 was be VBD 10_1101-2020_10_26_351783 42 4 not not RB 10_1101-2020_10_26_351783 42 5 certified certify VBN 10_1101-2020_10_26_351783 42 6 by by IN 10_1101-2020_10_26_351783 42 7 peer peer NN 10_1101-2020_10_26_351783 42 8 review review NN 10_1101-2020_10_26_351783 42 9 ) ) -RRB- 10_1101-2020_10_26_351783 42 10 is be VBZ 10_1101-2020_10_26_351783 42 11 the the DT 10_1101-2020_10_26_351783 42 12 author author NN 10_1101-2020_10_26_351783 42 13 / / SYM 10_1101-2020_10_26_351783 42 14 funder funder NN 10_1101-2020_10_26_351783 42 15 . . . 10_1101-2020_10_26_351783 43 1 All all DT 10_1101-2020_10_26_351783 43 2 rights right NNS 10_1101-2020_10_26_351783 43 3 reserved reserve VBD 10_1101-2020_10_26_351783 43 4 . . . 10_1101-2020_10_26_351783 44 1 No no DT 10_1101-2020_10_26_351783 44 2 reuse reuse NN 10_1101-2020_10_26_351783 44 3 allowed allow VBN 10_1101-2020_10_26_351783 44 4 without without IN 10_1101-2020_10_26_351783 44 5 permission permission NN 10_1101-2020_10_26_351783 44 6 . . . 10_1101-2020_10_26_351783 45 1 The the DT 10_1101-2020_10_26_351783 45 2 copyright copyright NN 10_1101-2020_10_26_351783 45 3 holder holder NN 10_1101-2020_10_26_351783 45 4 for for IN 10_1101-2020_10_26_351783 45 5 this this DT 10_1101-2020_10_26_351783 45 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 45 7 version version NN 10_1101-2020_10_26_351783 45 8 posted post VBD 10_1101-2020_10_26_351783 45 9 January January NNP 10_1101-2020_10_26_351783 45 10 6 6 CD 10_1101-2020_10_26_351783 45 11 , , , 10_1101-2020_10_26_351783 45 12 2021 2021 CD 10_1101-2020_10_26_351783 45 13 . . . 10_1101-2020_10_26_351783 45 14 ; ; : 10_1101-2020_10_26_351783 45 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 45 16 : : : 10_1101-2020_10_26_351783 45 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 45 18 preprint preprint NN 10_1101-2020_10_26_351783 45 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 45 20 5 5 CD 10_1101-2020_10_26_351783 45 21 MATERIALS material NNS 10_1101-2020_10_26_351783 45 22 AND and CC 10_1101-2020_10_26_351783 45 23 METHODS methods JJ 10_1101-2020_10_26_351783 45 24 Benchmark benchmark JJ 10_1101-2020_10_26_351783 45 25 data datum NNS 10_1101-2020_10_26_351783 45 26 A a DT 10_1101-2020_10_26_351783 45 27 total total NN 10_1101-2020_10_26_351783 45 28 of of IN 10_1101-2020_10_26_351783 45 29 47 47 CD 10_1101-2020_10_26_351783 45 30 publicly publicly RB 10_1101-2020_10_26_351783 45 31 available available JJ 10_1101-2020_10_26_351783 45 32 datasets dataset NNS 10_1101-2020_10_26_351783 45 33 for for IN 10_1101-2020_10_26_351783 45 34 the the DT 10_1101-2020_10_26_351783 45 35 transcriptomic transcriptomic NNP 10_1101-2020_10_26_351783 45 36 benchmark benchmark NN 10_1101-2020_10_26_351783 45 37 and and CC 10_1101-2020_10_26_351783 45 38 ten ten CD 10_1101-2020_10_26_351783 45 39 publicly publicly RB 10_1101-2020_10_26_351783 45 40 available available JJ 10_1101-2020_10_26_351783 45 41 datasets dataset NNS 10_1101-2020_10_26_351783 45 42 for for IN 10_1101-2020_10_26_351783 45 43 the the DT 10_1101-2020_10_26_351783 45 44 methylomic methylomic JJ 10_1101-2020_10_26_351783 45 45 benchmark benchmark NN 10_1101-2020_10_26_351783 45 46 were be VBD 10_1101-2020_10_26_351783 45 47 used use VBN 10_1101-2020_10_26_351783 45 48 . . . 10_1101-2020_10_26_351783 46 1 To to TO 10_1101-2020_10_26_351783 46 2 avoid avoid VB 10_1101-2020_10_26_351783 46 3 bias bias NN 10_1101-2020_10_26_351783 46 4 due due IN 10_1101-2020_10_26_351783 46 5 to to IN 10_1101-2020_10_26_351783 46 6 subtypes subtype NNS 10_1101-2020_10_26_351783 46 7 of of IN 10_1101-2020_10_26_351783 46 8 diseases disease NNS 10_1101-2020_10_26_351783 46 9 and and CC 10_1101-2020_10_26_351783 46 10 drug drug NN 10_1101-2020_10_26_351783 46 11 treatments treatment NNS 10_1101-2020_10_26_351783 46 12 , , , 10_1101-2020_10_26_351783 46 13 we -PRON- PRP 10_1101-2020_10_26_351783 46 14 searched search VBD 10_1101-2020_10_26_351783 46 15 for for IN 10_1101-2020_10_26_351783 46 16 datasets dataset NNS 10_1101-2020_10_26_351783 46 17 that that WDT 10_1101-2020_10_26_351783 46 18 have have VBP 10_1101-2020_10_26_351783 46 19 only only JJ 10_1101-2020_10_26_351783 46 20 patient patient NN 10_1101-2020_10_26_351783 46 21 and and CC 10_1101-2020_10_26_351783 46 22 control control NN 10_1101-2020_10_26_351783 46 23 samples sample NNS 10_1101-2020_10_26_351783 46 24 , , , 10_1101-2020_10_26_351783 46 25 and and CC 10_1101-2020_10_26_351783 46 26 that that WDT 10_1101-2020_10_26_351783 46 27 are be VBP 10_1101-2020_10_26_351783 46 28 available available JJ 10_1101-2020_10_26_351783 46 29 for for IN 10_1101-2020_10_26_351783 46 30 download download NN 10_1101-2020_10_26_351783 46 31 from from IN 10_1101-2020_10_26_351783 46 32 the the DT 10_1101-2020_10_26_351783 46 33 GEO GEO NNP 10_1101-2020_10_26_351783 46 34 database database NN 10_1101-2020_10_26_351783 46 35 . . . 10_1101-2020_10_26_351783 47 1 We -PRON- PRP 10_1101-2020_10_26_351783 47 2 categorized categorize VBD 10_1101-2020_10_26_351783 47 3 the the DT 10_1101-2020_10_26_351783 47 4 datasets dataset NNS 10_1101-2020_10_26_351783 47 5 into into IN 10_1101-2020_10_26_351783 47 6 seven seven CD 10_1101-2020_10_26_351783 47 7 distinct distinct JJ 10_1101-2020_10_26_351783 47 8 disease disease NN 10_1101-2020_10_26_351783 47 9 types type NNS 10_1101-2020_10_26_351783 47 10 based base VBN 10_1101-2020_10_26_351783 47 11 on on IN 10_1101-2020_10_26_351783 47 12 the the DT 10_1101-2020_10_26_351783 47 13 disease disease NN 10_1101-2020_10_26_351783 47 14 - - HYPH 10_1101-2020_10_26_351783 47 15 trait trait NN 10_1101-2020_10_26_351783 47 16 type type NN 10_1101-2020_10_26_351783 47 17 associations association NNS 10_1101-2020_10_26_351783 47 18 used use VBN 10_1101-2020_10_26_351783 47 19 in in IN 10_1101-2020_10_26_351783 47 20 Choobdar Choobdar NNP 10_1101-2020_10_26_351783 47 21 et et NNP 10_1101-2020_10_26_351783 47 22 al[12 al[12 NNP 10_1101-2020_10_26_351783 47 23 ] ] -RRB- 10_1101-2020_10_26_351783 47 24 . . . 10_1101-2020_10_26_351783 47 25 , , , 10_1101-2020_10_26_351783 47 26 i.e. i.e. FW 10_1101-2020_10_26_351783 48 1 autoimmune autoimmune NNP 10_1101-2020_10_26_351783 48 2 , , , 10_1101-2020_10_26_351783 48 3 cardiovascular cardiovascular NNP 10_1101-2020_10_26_351783 48 4 , , , 10_1101-2020_10_26_351783 48 5 glycemic glycemic JJ 10_1101-2020_10_26_351783 48 6 , , , 10_1101-2020_10_26_351783 48 7 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 48 8 , , , 10_1101-2020_10_26_351783 48 9 neurodegenerative neurodegenerative JJ 10_1101-2020_10_26_351783 48 10 , , , 10_1101-2020_10_26_351783 48 11 and and CC 10_1101-2020_10_26_351783 48 12 psychiatric psychiatric JJ 10_1101-2020_10_26_351783 48 13 and and CC 10_1101-2020_10_26_351783 48 14 social social JJ 10_1101-2020_10_26_351783 48 15 disorders disorder NNS 10_1101-2020_10_26_351783 48 16 . . . 10_1101-2020_10_26_351783 49 1 A a DT 10_1101-2020_10_26_351783 49 2 total total NN 10_1101-2020_10_26_351783 49 3 of of IN 10_1101-2020_10_26_351783 49 4 19 19 CD 10_1101-2020_10_26_351783 49 5 complex complex JJ 10_1101-2020_10_26_351783 49 6 diseases disease NNS 10_1101-2020_10_26_351783 49 7 were be VBD 10_1101-2020_10_26_351783 49 8 used use VBN 10_1101-2020_10_26_351783 49 9 in in IN 10_1101-2020_10_26_351783 49 10 the the DT 10_1101-2020_10_26_351783 49 11 transcriptomic transcriptomic NNP 10_1101-2020_10_26_351783 49 12 benchmark benchmark NN 10_1101-2020_10_26_351783 49 13 analysis analysis NN 10_1101-2020_10_26_351783 49 14 , , , 10_1101-2020_10_26_351783 49 15 while while IN 10_1101-2020_10_26_351783 49 16 six six CD 10_1101-2020_10_26_351783 49 17 complex complex JJ 10_1101-2020_10_26_351783 49 18 diseases disease NNS 10_1101-2020_10_26_351783 49 19 were be VBD 10_1101-2020_10_26_351783 49 20 used use VBN 10_1101-2020_10_26_351783 49 21 in in IN 10_1101-2020_10_26_351783 49 22 the the DT 10_1101-2020_10_26_351783 49 23 methylation methylation NN 10_1101-2020_10_26_351783 49 24 benchmark benchmark NN 10_1101-2020_10_26_351783 49 25 analysis analysis NN 10_1101-2020_10_26_351783 49 26 . . . 10_1101-2020_10_26_351783 50 1 The the DT 10_1101-2020_10_26_351783 50 2 methylation methylation NN 10_1101-2020_10_26_351783 50 3 benchmark benchmark NN 10_1101-2020_10_26_351783 50 4 diseases disease NNS 10_1101-2020_10_26_351783 50 5 belong belong VBP 10_1101-2020_10_26_351783 50 6 to to IN 10_1101-2020_10_26_351783 50 7 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 50 8 , , , 10_1101-2020_10_26_351783 50 9 autoimmune autoimmune NNP 10_1101-2020_10_26_351783 50 10 , , , 10_1101-2020_10_26_351783 50 11 and and CC 10_1101-2020_10_26_351783 50 12 glycemic glycemic JJ 10_1101-2020_10_26_351783 50 13 disease disease NN 10_1101-2020_10_26_351783 50 14 types type NNS 10_1101-2020_10_26_351783 50 15 . . . 10_1101-2020_10_26_351783 51 1 MS MS NNP 10_1101-2020_10_26_351783 51 2 use use VBP 10_1101-2020_10_26_351783 51 3 case case NN 10_1101-2020_10_26_351783 51 4 data datum NNS 10_1101-2020_10_26_351783 51 5 A a DT 10_1101-2020_10_26_351783 51 6 total total NN 10_1101-2020_10_26_351783 51 7 of of IN 10_1101-2020_10_26_351783 51 8 14 14 CD 10_1101-2020_10_26_351783 51 9 publicly publicly RB 10_1101-2020_10_26_351783 51 10 available available JJ 10_1101-2020_10_26_351783 51 11 and and CC 10_1101-2020_10_26_351783 51 12 one one CD 10_1101-2020_10_26_351783 51 13 non non JJ 10_1101-2020_10_26_351783 51 14 - - JJ 10_1101-2020_10_26_351783 51 15 publicly publicly RB 10_1101-2020_10_26_351783 51 16 available available JJ 10_1101-2020_10_26_351783 51 17 transcriptomic transcriptomic NN 10_1101-2020_10_26_351783 51 18 and and CC 10_1101-2020_10_26_351783 51 19 methylomic methylomic JJ 10_1101-2020_10_26_351783 51 20 MS- ms- JJ 10_1101-2020_10_26_351783 51 21 related relate VBN 10_1101-2020_10_26_351783 51 22 datasets dataset NNS 10_1101-2020_10_26_351783 51 23 were be VBD 10_1101-2020_10_26_351783 51 24 used use VBN 10_1101-2020_10_26_351783 51 25 in in IN 10_1101-2020_10_26_351783 51 26 the the DT 10_1101-2020_10_26_351783 51 27 MS MS NNP 10_1101-2020_10_26_351783 51 28 multi multi JJ 10_1101-2020_10_26_351783 51 29 - - HYPH 10_1101-2020_10_26_351783 51 30 omics omic NNS 10_1101-2020_10_26_351783 51 31 integration integration NN 10_1101-2020_10_26_351783 51 32 use use NN 10_1101-2020_10_26_351783 51 33 case case NN 10_1101-2020_10_26_351783 51 34 . . . 10_1101-2020_10_26_351783 52 1 In in IN 10_1101-2020_10_26_351783 52 2 general general JJ 10_1101-2020_10_26_351783 52 3 , , , 10_1101-2020_10_26_351783 52 4 every every DT 10_1101-2020_10_26_351783 52 5 dataset dataset NN 10_1101-2020_10_26_351783 52 6 in in IN 10_1101-2020_10_26_351783 52 7 the the DT 10_1101-2020_10_26_351783 52 8 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 52 9 benchmark benchmark NN 10_1101-2020_10_26_351783 52 10 was be VBD 10_1101-2020_10_26_351783 52 11 also also RB 10_1101-2020_10_26_351783 52 12 used use VBN 10_1101-2020_10_26_351783 52 13 in in IN 10_1101-2020_10_26_351783 52 14 the the DT 10_1101-2020_10_26_351783 52 15 MS MS NNP 10_1101-2020_10_26_351783 52 16 use use NN 10_1101-2020_10_26_351783 52 17 case case NN 10_1101-2020_10_26_351783 52 18 , , , 10_1101-2020_10_26_351783 52 19 with with IN 10_1101-2020_10_26_351783 52 20 exceptions exception NNS 10_1101-2020_10_26_351783 52 21 according accord VBG 10_1101-2020_10_26_351783 52 22 to to IN 10_1101-2020_10_26_351783 52 23 certain certain JJ 10_1101-2020_10_26_351783 52 24 criteria criterion NNS 10_1101-2020_10_26_351783 52 25 . . . 10_1101-2020_10_26_351783 53 1 The the DT 10_1101-2020_10_26_351783 53 2 inclusion inclusion NN 10_1101-2020_10_26_351783 53 3 of of IN 10_1101-2020_10_26_351783 53 4 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 53 5 MS MS NNP 10_1101-2020_10_26_351783 53 6 datasets dataset NNS 10_1101-2020_10_26_351783 53 7 followed follow VBD 10_1101-2020_10_26_351783 53 8 the the DT 10_1101-2020_10_26_351783 53 9 criteria criterion NNS 10_1101-2020_10_26_351783 53 10 : : : 10_1101-2020_10_26_351783 53 11 1 1 LS 10_1101-2020_10_26_351783 53 12 ) ) -RRB- 10_1101-2020_10_26_351783 53 13 The the DT 10_1101-2020_10_26_351783 53 14 largest large JJS 10_1101-2020_10_26_351783 53 15 dataset dataset NN 10_1101-2020_10_26_351783 53 16 by by IN 10_1101-2020_10_26_351783 53 17 sample sample NN 10_1101-2020_10_26_351783 53 18 number number NN 10_1101-2020_10_26_351783 53 19 , , , 10_1101-2020_10_26_351783 53 20 per per IN 10_1101-2020_10_26_351783 53 21 tissue tissue NN 10_1101-2020_10_26_351783 53 22 , , , 10_1101-2020_10_26_351783 53 23 is be VBZ 10_1101-2020_10_26_351783 53 24 shown show VBN 10_1101-2020_10_26_351783 53 25 in in IN 10_1101-2020_10_26_351783 53 26 the the DT 10_1101-2020_10_26_351783 53 27 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 53 28 benchmark benchmark NN 10_1101-2020_10_26_351783 53 29 ; ; : 10_1101-2020_10_26_351783 53 30 2 2 LS 10_1101-2020_10_26_351783 53 31 ) ) -RRB- 10_1101-2020_10_26_351783 53 32 Replication replication NN 10_1101-2020_10_26_351783 53 33 cohorts cohort NNS 10_1101-2020_10_26_351783 53 34 are be VBP 10_1101-2020_10_26_351783 53 35 not not RB 10_1101-2020_10_26_351783 53 36 included include VBN 10_1101-2020_10_26_351783 53 37 in in IN 10_1101-2020_10_26_351783 53 38 the the DT 10_1101-2020_10_26_351783 53 39 MS MS NNP 10_1101-2020_10_26_351783 53 40 use use NN 10_1101-2020_10_26_351783 53 41 case case NN 10_1101-2020_10_26_351783 53 42 . . . 10_1101-2020_10_26_351783 54 1 Criteria criterion NNS 10_1101-2020_10_26_351783 54 2 for for IN 10_1101-2020_10_26_351783 54 3 inclusion inclusion NN 10_1101-2020_10_26_351783 54 4 of of IN 10_1101-2020_10_26_351783 54 5 methylomic methylomic JJ 10_1101-2020_10_26_351783 54 6 MS MS NNP 10_1101-2020_10_26_351783 54 7 datasets dataset NNS 10_1101-2020_10_26_351783 54 8 were be VBD 10_1101-2020_10_26_351783 54 9 the the DT 10_1101-2020_10_26_351783 54 10 following follow VBG 10_1101-2020_10_26_351783 54 11 : : : 10_1101-2020_10_26_351783 54 12 1 1 LS 10_1101-2020_10_26_351783 54 13 ) ) -RRB- 10_1101-2020_10_26_351783 54 14 The the DT 10_1101-2020_10_26_351783 54 15 largest large JJS 10_1101-2020_10_26_351783 54 16 dataset dataset NN 10_1101-2020_10_26_351783 54 17 by by IN 10_1101-2020_10_26_351783 54 18 sample sample NN 10_1101-2020_10_26_351783 54 19 number number NN 10_1101-2020_10_26_351783 54 20 , , , 10_1101-2020_10_26_351783 54 21 per per IN 10_1101-2020_10_26_351783 54 22 tissue tissue NN 10_1101-2020_10_26_351783 54 23 or or CC 10_1101-2020_10_26_351783 54 24 cell cell NN 10_1101-2020_10_26_351783 54 25 type type NN 10_1101-2020_10_26_351783 54 26 , , , 10_1101-2020_10_26_351783 54 27 is be VBZ 10_1101-2020_10_26_351783 54 28 included include VBN 10_1101-2020_10_26_351783 54 29 in in IN 10_1101-2020_10_26_351783 54 30 the the DT 10_1101-2020_10_26_351783 54 31 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 54 32 benchmark benchmark NN 10_1101-2020_10_26_351783 54 33 ; ; : 10_1101-2020_10_26_351783 54 34 2 2 LS 10_1101-2020_10_26_351783 54 35 ) ) -RRB- 10_1101-2020_10_26_351783 54 36 A a DT 10_1101-2020_10_26_351783 54 37 single single JJ 10_1101-2020_10_26_351783 54 38 dataset dataset NN 10_1101-2020_10_26_351783 54 39 for for IN 10_1101-2020_10_26_351783 54 40 every every DT 10_1101-2020_10_26_351783 54 41 cell cell NN 10_1101-2020_10_26_351783 54 42 - - HYPH 10_1101-2020_10_26_351783 54 43 specific specific JJ 10_1101-2020_10_26_351783 54 44 tissue tissue NN 10_1101-2020_10_26_351783 54 45 was be VBD 10_1101-2020_10_26_351783 54 46 included include VBN 10_1101-2020_10_26_351783 54 47 in in IN 10_1101-2020_10_26_351783 54 48 the the DT 10_1101-2020_10_26_351783 54 49 benchmark benchmark NN 10_1101-2020_10_26_351783 54 50 ; ; : 10_1101-2020_10_26_351783 54 51 3 3 LS 10_1101-2020_10_26_351783 54 52 ) ) -RRB- 10_1101-2020_10_26_351783 54 53 Methylation methylation NN 10_1101-2020_10_26_351783 54 54 studies study NNS 10_1101-2020_10_26_351783 54 55 that that WDT 10_1101-2020_10_26_351783 54 56 reported report VBD 10_1101-2020_10_26_351783 54 57 using use VBG 10_1101-2020_10_26_351783 54 58 whole whole JJ 10_1101-2020_10_26_351783 54 59 blood blood NN 10_1101-2020_10_26_351783 54 60 as as IN 10_1101-2020_10_26_351783 54 61 sample sample NN 10_1101-2020_10_26_351783 54 62 tissue tissue NN 10_1101-2020_10_26_351783 54 63 were be VBD 10_1101-2020_10_26_351783 54 64 excluded exclude VBN 10_1101-2020_10_26_351783 54 65 from from IN 10_1101-2020_10_26_351783 54 66 the the DT 10_1101-2020_10_26_351783 54 67 MS MS NNP 10_1101-2020_10_26_351783 54 68 use use NN 10_1101-2020_10_26_351783 54 69 case case NN 10_1101-2020_10_26_351783 54 70 , , , 10_1101-2020_10_26_351783 54 71 due due IN 10_1101-2020_10_26_351783 54 72 to to IN 10_1101-2020_10_26_351783 54 73 the the DT 10_1101-2020_10_26_351783 54 74 high high JJ 10_1101-2020_10_26_351783 54 75 heterogeneity heterogeneity NN 10_1101-2020_10_26_351783 54 76 of of IN 10_1101-2020_10_26_351783 54 77 this this DT 10_1101-2020_10_26_351783 54 78 type type NN 10_1101-2020_10_26_351783 54 79 of of IN 10_1101-2020_10_26_351783 54 80 data datum NNS 10_1101-2020_10_26_351783 54 81 . . . 10_1101-2020_10_26_351783 55 1 For for IN 10_1101-2020_10_26_351783 55 2 the the DT 10_1101-2020_10_26_351783 55 3 additional additional JJ 10_1101-2020_10_26_351783 55 4 independent independent JJ 10_1101-2020_10_26_351783 55 5 validation validation NN 10_1101-2020_10_26_351783 55 6 , , , 10_1101-2020_10_26_351783 55 7 we -PRON- PRP 10_1101-2020_10_26_351783 55 8 utilized utilize VBD 10_1101-2020_10_26_351783 55 9 the the DT 10_1101-2020_10_26_351783 55 10 methylation methylation NN 10_1101-2020_10_26_351783 55 11 microarray microarray JJ 10_1101-2020_10_26_351783 55 12 analysis analysis NN 10_1101-2020_10_26_351783 55 13 of of IN 10_1101-2020_10_26_351783 55 14 279 279 CD 10_1101-2020_10_26_351783 55 15 blood blood NN 10_1101-2020_10_26_351783 55 16 samples sample NNS 10_1101-2020_10_26_351783 55 17 analyzing analyze VBG 10_1101-2020_10_26_351783 55 18 from from IN 10_1101-2020_10_26_351783 55 19 Kular Kular NNP 10_1101-2020_10_26_351783 55 20 et et NNP 10_1101-2020_10_26_351783 55 21 al al NNP 10_1101-2020_10_26_351783 55 22 25 25 CD 10_1101-2020_10_26_351783 55 23 . . . 10_1101-2020_10_26_351783 56 1 For for IN 10_1101-2020_10_26_351783 56 2 each each DT 10_1101-2020_10_26_351783 56 3 of of IN 10_1101-2020_10_26_351783 56 4 these these DT 10_1101-2020_10_26_351783 56 5 MS MS NNP 10_1101-2020_10_26_351783 56 6 patients patient NNS 10_1101-2020_10_26_351783 56 7 ( ( -LRB- 10_1101-2020_10_26_351783 56 8 nMS= nMS= NNP 10_1101-2020_10_26_351783 56 9 139 139 CD 10_1101-2020_10_26_351783 56 10 ) ) -RRB- 10_1101-2020_10_26_351783 56 11 and and CC 10_1101-2020_10_26_351783 56 12 healthy healthy JJ 10_1101-2020_10_26_351783 56 13 controls control NNS 10_1101-2020_10_26_351783 56 14 ( ( -LRB- 10_1101-2020_10_26_351783 56 15 nHC= nhc= IN 10_1101-2020_10_26_351783 56 16 140 140 CD 10_1101-2020_10_26_351783 56 17 ) ) -RRB- 10_1101-2020_10_26_351783 56 18 , , , 10_1101-2020_10_26_351783 56 19 we -PRON- PRP 10_1101-2020_10_26_351783 56 20 also also RB 10_1101-2020_10_26_351783 56 21 collected collect VBD 10_1101-2020_10_26_351783 56 22 their -PRON- PRP$ 10_1101-2020_10_26_351783 56 23 lifestyle lifestyle NN 10_1101-2020_10_26_351783 56 24 - - HYPH 10_1101-2020_10_26_351783 56 25 associated associate VBN 10_1101-2020_10_26_351783 56 26 risk risk NN 10_1101-2020_10_26_351783 56 27 factors factor NNS 10_1101-2020_10_26_351783 56 28 from from IN 10_1101-2020_10_26_351783 56 29 questionnaires questionnaire NNS 10_1101-2020_10_26_351783 56 30 that that WDT 10_1101-2020_10_26_351783 56 31 ( ( -LRB- 10_1101-2020_10_26_351783 56 32 which which WDT 10_1101-2020_10_26_351783 56 33 was be VBD 10_1101-2020_10_26_351783 56 34 not not RB 10_1101-2020_10_26_351783 56 35 certified certify VBN 10_1101-2020_10_26_351783 56 36 by by IN 10_1101-2020_10_26_351783 56 37 peer peer NN 10_1101-2020_10_26_351783 56 38 review review NN 10_1101-2020_10_26_351783 56 39 ) ) -RRB- 10_1101-2020_10_26_351783 56 40 is be VBZ 10_1101-2020_10_26_351783 56 41 the the DT 10_1101-2020_10_26_351783 56 42 author author NN 10_1101-2020_10_26_351783 56 43 / / SYM 10_1101-2020_10_26_351783 56 44 funder funder NN 10_1101-2020_10_26_351783 56 45 . . . 10_1101-2020_10_26_351783 57 1 All all DT 10_1101-2020_10_26_351783 57 2 rights right NNS 10_1101-2020_10_26_351783 57 3 reserved reserve VBD 10_1101-2020_10_26_351783 57 4 . . . 10_1101-2020_10_26_351783 58 1 No no DT 10_1101-2020_10_26_351783 58 2 reuse reuse NN 10_1101-2020_10_26_351783 58 3 allowed allow VBN 10_1101-2020_10_26_351783 58 4 without without IN 10_1101-2020_10_26_351783 58 5 permission permission NN 10_1101-2020_10_26_351783 58 6 . . . 10_1101-2020_10_26_351783 59 1 The the DT 10_1101-2020_10_26_351783 59 2 copyright copyright NN 10_1101-2020_10_26_351783 59 3 holder holder NN 10_1101-2020_10_26_351783 59 4 for for IN 10_1101-2020_10_26_351783 59 5 this this DT 10_1101-2020_10_26_351783 59 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 59 7 version version NN 10_1101-2020_10_26_351783 59 8 posted post VBD 10_1101-2020_10_26_351783 59 9 January January NNP 10_1101-2020_10_26_351783 59 10 6 6 CD 10_1101-2020_10_26_351783 59 11 , , , 10_1101-2020_10_26_351783 59 12 2021 2021 CD 10_1101-2020_10_26_351783 59 13 . . . 10_1101-2020_10_26_351783 59 14 ; ; : 10_1101-2020_10_26_351783 59 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 59 16 : : : 10_1101-2020_10_26_351783 59 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 59 18 preprint preprint NN 10_1101-2020_10_26_351783 59 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 59 20 6 6 CD 10_1101-2020_10_26_351783 59 21 were be VBD 10_1101-2020_10_26_351783 59 22 part part NN 10_1101-2020_10_26_351783 59 23 of of IN 10_1101-2020_10_26_351783 59 24 the the DT 10_1101-2020_10_26_351783 59 25 Epidemiological Epidemiological NNP 10_1101-2020_10_26_351783 59 26 Investigation Investigation NNP 10_1101-2020_10_26_351783 59 27 of of IN 10_1101-2020_10_26_351783 59 28 Multiple Multiple NNP 10_1101-2020_10_26_351783 59 29 Sclerosis Sclerosis NNP 10_1101-2020_10_26_351783 59 30 ( ( -LRB- 10_1101-2020_10_26_351783 59 31 EIMS eims NN 10_1101-2020_10_26_351783 59 32 ) ) -RRB- 10_1101-2020_10_26_351783 59 33 study study NN 10_1101-2020_10_26_351783 59 34 . . . 10_1101-2020_10_26_351783 60 1 Those those DT 10_1101-2020_10_26_351783 60 2 factors factor NNS 10_1101-2020_10_26_351783 60 3 were be VBD 10_1101-2020_10_26_351783 60 4 smoking smoke VBG 10_1101-2020_10_26_351783 60 5 status status NN 10_1101-2020_10_26_351783 60 6 , , , 10_1101-2020_10_26_351783 60 7 prior prior RB 10_1101-2020_10_26_351783 60 8 EBV EBV NNP 10_1101-2020_10_26_351783 60 9 infection infection NN 10_1101-2020_10_26_351783 60 10 , , , 10_1101-2020_10_26_351783 60 11 sunbathing sunbathing NN 10_1101-2020_10_26_351783 60 12 , , , 10_1101-2020_10_26_351783 60 13 nightshift nightshift JJ 10_1101-2020_10_26_351783 60 14 work work NN 10_1101-2020_10_26_351783 60 15 , , , 10_1101-2020_10_26_351783 60 16 alcohol alcohol NN 10_1101-2020_10_26_351783 60 17 consumption consumption NN 10_1101-2020_10_26_351783 60 18 , , , 10_1101-2020_10_26_351783 60 19 as as RB 10_1101-2020_10_26_351783 60 20 well well RB 10_1101-2020_10_26_351783 60 21 as as IN 10_1101-2020_10_26_351783 60 22 phenotypic phenotypic NN 10_1101-2020_10_26_351783 60 23 features feature NNS 10_1101-2020_10_26_351783 60 24 ( ( -LRB- 10_1101-2020_10_26_351783 60 25 age age NN 10_1101-2020_10_26_351783 60 26 , , , 10_1101-2020_10_26_351783 60 27 sex sex NN 10_1101-2020_10_26_351783 60 28 , , , 10_1101-2020_10_26_351783 60 29 BMI BMI NNP 10_1101-2020_10_26_351783 60 30 at at IN 10_1101-2020_10_26_351783 60 31 age age NN 10_1101-2020_10_26_351783 60 32 of of IN 10_1101-2020_10_26_351783 60 33 20 20 CD 10_1101-2020_10_26_351783 60 34 ) ) -RRB- 10_1101-2020_10_26_351783 60 35 . . . 10_1101-2020_10_26_351783 61 1 Pre pre JJ 10_1101-2020_10_26_351783 61 2 - - JJ 10_1101-2020_10_26_351783 61 3 processing processing NN 10_1101-2020_10_26_351783 61 4 and and CC 10_1101-2020_10_26_351783 61 5 quality quality NN 10_1101-2020_10_26_351783 61 6 control control NN 10_1101-2020_10_26_351783 61 7 of of IN 10_1101-2020_10_26_351783 61 8 risk risk NN 10_1101-2020_10_26_351783 61 9 factor factor NN 10_1101-2020_10_26_351783 61 10 methylation methylation NN 10_1101-2020_10_26_351783 61 11 data datum NNS 10_1101-2020_10_26_351783 61 12 DNA dna NN 10_1101-2020_10_26_351783 61 13 methylation methylation NN 10_1101-2020_10_26_351783 61 14 datasets dataset NNS 10_1101-2020_10_26_351783 61 15 were be VBD 10_1101-2020_10_26_351783 61 16 downloaded download VBN 10_1101-2020_10_26_351783 61 17 from from IN 10_1101-2020_10_26_351783 61 18 GEO GEO NNP 10_1101-2020_10_26_351783 61 19 as as IN 10_1101-2020_10_26_351783 61 20 raw raw JJ 10_1101-2020_10_26_351783 61 21 IDAT IDAT NNP 10_1101-2020_10_26_351783 61 22 files file NNS 10_1101-2020_10_26_351783 61 23 , , , 10_1101-2020_10_26_351783 61 24 when when WRB 10_1101-2020_10_26_351783 61 25 available available JJ 10_1101-2020_10_26_351783 61 26 , , , 10_1101-2020_10_26_351783 61 27 or or CC 10_1101-2020_10_26_351783 61 28 matrices matrix NNS 10_1101-2020_10_26_351783 61 29 of of IN 10_1101-2020_10_26_351783 61 30 beta beta JJ 10_1101-2020_10_26_351783 61 31 values value NNS 10_1101-2020_10_26_351783 61 32 . . . 10_1101-2020_10_26_351783 62 1 Pre pre JJ 10_1101-2020_10_26_351783 62 2 - - JJ 10_1101-2020_10_26_351783 62 3 processing processing NN 10_1101-2020_10_26_351783 62 4 of of IN 10_1101-2020_10_26_351783 62 5 the the DT 10_1101-2020_10_26_351783 62 6 data datum NNS 10_1101-2020_10_26_351783 62 7 was be VBD 10_1101-2020_10_26_351783 62 8 performed perform VBN 10_1101-2020_10_26_351783 62 9 using use VBG 10_1101-2020_10_26_351783 62 10 the the DT 10_1101-2020_10_26_351783 62 11 Chip Chip NNP 10_1101-2020_10_26_351783 62 12 Analysis Analysis NNP 10_1101-2020_10_26_351783 62 13 Methylation Methylation NNP 10_1101-2020_10_26_351783 62 14 Pipeline Pipeline NNP 10_1101-2020_10_26_351783 62 15 ( ( -LRB- 10_1101-2020_10_26_351783 62 16 ChAMP ChAMP NNP 10_1101-2020_10_26_351783 62 17 ) ) -RRB- 10_1101-2020_10_26_351783 62 18 R R NNP 10_1101-2020_10_26_351783 62 19 package[14 package[14 RB 10_1101-2020_10_26_351783 62 20 ] ] -RRB- 10_1101-2020_10_26_351783 62 21 , , , 10_1101-2020_10_26_351783 62 22 version version NN 10_1101-2020_10_26_351783 62 23 2.16.2 2.16.2 CD 10_1101-2020_10_26_351783 62 24 . . . 10_1101-2020_10_26_351783 63 1 Default default NN 10_1101-2020_10_26_351783 63 2 parameters parameter NNS 10_1101-2020_10_26_351783 63 3 were be VBD 10_1101-2020_10_26_351783 63 4 used use VBN 10_1101-2020_10_26_351783 63 5 for for IN 10_1101-2020_10_26_351783 63 6 probe probe NN 10_1101-2020_10_26_351783 63 7 and and CC 10_1101-2020_10_26_351783 63 8 sample sample NN 10_1101-2020_10_26_351783 63 9 filtering filtering NN 10_1101-2020_10_26_351783 63 10 . . . 10_1101-2020_10_26_351783 64 1 Probes probe NNS 10_1101-2020_10_26_351783 64 2 with with IN 10_1101-2020_10_26_351783 64 3 a a DT 10_1101-2020_10_26_351783 64 4 detection detection NN 10_1101-2020_10_26_351783 64 5 P p NN 10_1101-2020_10_26_351783 64 6 - - HYPH 10_1101-2020_10_26_351783 64 7 value value NN 10_1101-2020_10_26_351783 64 8 above above IN 10_1101-2020_10_26_351783 64 9 0.01 0.01 CD 10_1101-2020_10_26_351783 64 10 , , , 10_1101-2020_10_26_351783 64 11 probes probe NNS 10_1101-2020_10_26_351783 64 12 with with IN 10_1101-2020_10_26_351783 64 13 a a DT 10_1101-2020_10_26_351783 64 14 fraction fraction NN 10_1101-2020_10_26_351783 64 15 of of IN 10_1101-2020_10_26_351783 64 16 failed fail VBN 10_1101-2020_10_26_351783 64 17 ( ( -LRB- 10_1101-2020_10_26_351783 64 18 bead bead NNP 10_1101-2020_10_26_351783 64 19 count count NNP 10_1101-2020_10_26_351783 64 20 less less JJR 10_1101-2020_10_26_351783 64 21 than than IN 10_1101-2020_10_26_351783 64 22 3 3 CD 10_1101-2020_10_26_351783 64 23 ) ) -RRB- 10_1101-2020_10_26_351783 64 24 samples sample NNS 10_1101-2020_10_26_351783 64 25 over over IN 10_1101-2020_10_26_351783 64 26 0.05 0.05 CD 10_1101-2020_10_26_351783 64 27 , , , 10_1101-2020_10_26_351783 64 28 non non JJ 10_1101-2020_10_26_351783 64 29 - - JJ 10_1101-2020_10_26_351783 64 30 CpG cpg JJ 10_1101-2020_10_26_351783 64 31 probes probe NNS 10_1101-2020_10_26_351783 64 32 , , , 10_1101-2020_10_26_351783 64 33 SNP SNP NNP 10_1101-2020_10_26_351783 64 34 - - HYPH 10_1101-2020_10_26_351783 64 35 related relate VBN 10_1101-2020_10_26_351783 64 36 probes probe NNS 10_1101-2020_10_26_351783 64 37 , , , 10_1101-2020_10_26_351783 64 38 multi multi JJ 10_1101-2020_10_26_351783 64 39 - - JJ 10_1101-2020_10_26_351783 64 40 hit hit VBN 10_1101-2020_10_26_351783 64 41 probes probe NNS 10_1101-2020_10_26_351783 64 42 , , , 10_1101-2020_10_26_351783 64 43 and and CC 10_1101-2020_10_26_351783 64 44 probes probe NNS 10_1101-2020_10_26_351783 64 45 located locate VBN 10_1101-2020_10_26_351783 64 46 on on IN 10_1101-2020_10_26_351783 64 47 chromosomes chromosome NNS 10_1101-2020_10_26_351783 64 48 X X NNP 10_1101-2020_10_26_351783 64 49 and and CC 10_1101-2020_10_26_351783 64 50 Y Y NNP 10_1101-2020_10_26_351783 64 51 , , , 10_1101-2020_10_26_351783 64 52 were be VBD 10_1101-2020_10_26_351783 64 53 removed remove VBN 10_1101-2020_10_26_351783 64 54 . . . 10_1101-2020_10_26_351783 65 1 Samples sample NNS 10_1101-2020_10_26_351783 65 2 with with IN 10_1101-2020_10_26_351783 65 3 a a DT 10_1101-2020_10_26_351783 65 4 proportion proportion NN 10_1101-2020_10_26_351783 65 5 of of IN 10_1101-2020_10_26_351783 65 6 failed fail VBN 10_1101-2020_10_26_351783 65 7 ( ( -LRB- 10_1101-2020_10_26_351783 65 8 NA NA NNP 10_1101-2020_10_26_351783 65 9 ) ) -RRB- 10_1101-2020_10_26_351783 65 10 probe probe NN 10_1101-2020_10_26_351783 65 11 P p NN 10_1101-2020_10_26_351783 65 12 - - HYPH 10_1101-2020_10_26_351783 65 13 values value NNS 10_1101-2020_10_26_351783 65 14 over over IN 10_1101-2020_10_26_351783 65 15 0.1 0.1 CD 10_1101-2020_10_26_351783 65 16 were be VBD 10_1101-2020_10_26_351783 65 17 also also RB 10_1101-2020_10_26_351783 65 18 removed remove VBN 10_1101-2020_10_26_351783 65 19 from from IN 10_1101-2020_10_26_351783 65 20 the the DT 10_1101-2020_10_26_351783 65 21 analysis analysis NN 10_1101-2020_10_26_351783 65 22 . . . 10_1101-2020_10_26_351783 66 1 Post post JJ 10_1101-2020_10_26_351783 66 2 - - JJ 10_1101-2020_10_26_351783 66 3 filtering filtering JJ 10_1101-2020_10_26_351783 66 4 imputation imputation NN 10_1101-2020_10_26_351783 66 5 of of IN 10_1101-2020_10_26_351783 66 6 NA NA NNP 10_1101-2020_10_26_351783 66 7 values value NNS 10_1101-2020_10_26_351783 66 8 was be VBD 10_1101-2020_10_26_351783 66 9 conducted conduct VBN 10_1101-2020_10_26_351783 66 10 on on IN 10_1101-2020_10_26_351783 66 11 the the DT 10_1101-2020_10_26_351783 66 12 beta beta JJ 10_1101-2020_10_26_351783 66 13 matrices matrix NNS 10_1101-2020_10_26_351783 66 14 , , , 10_1101-2020_10_26_351783 66 15 with with IN 10_1101-2020_10_26_351783 66 16 default default NN 10_1101-2020_10_26_351783 66 17 parameters parameter NNS 10_1101-2020_10_26_351783 66 18 ( ( -LRB- 10_1101-2020_10_26_351783 66 19 “ " `` 10_1101-2020_10_26_351783 66 20 combine combine VB 10_1101-2020_10_26_351783 66 21 ” " '' 10_1101-2020_10_26_351783 66 22 method method NN 10_1101-2020_10_26_351783 66 23 , , , 10_1101-2020_10_26_351783 66 24 k k NNP 10_1101-2020_10_26_351783 66 25 = = SYM 10_1101-2020_10_26_351783 66 26 5 5 CD 10_1101-2020_10_26_351783 66 27 , , , 10_1101-2020_10_26_351783 66 28 probe probe NNP 10_1101-2020_10_26_351783 66 29 cutoff cutoff NNP 10_1101-2020_10_26_351783 66 30 = = SYM 10_1101-2020_10_26_351783 66 31 0.2 0.2 CD 10_1101-2020_10_26_351783 66 32 , , , 10_1101-2020_10_26_351783 66 33 sample sample NN 10_1101-2020_10_26_351783 66 34 cutoff cutoff FW 10_1101-2020_10_26_351783 66 35 = = SYM 10_1101-2020_10_26_351783 66 36 0.1 0.1 CD 10_1101-2020_10_26_351783 66 37 ) ) -RRB- 10_1101-2020_10_26_351783 66 38 . . . 10_1101-2020_10_26_351783 67 1 Filtered filter VBN 10_1101-2020_10_26_351783 67 2 imputed imputed JJ 10_1101-2020_10_26_351783 67 3 matrices matrix NNS 10_1101-2020_10_26_351783 67 4 were be VBD 10_1101-2020_10_26_351783 67 5 normalized normalized JJ 10_1101-2020_10_26_351783 67 6 applying apply VBG 10_1101-2020_10_26_351783 67 7 the the DT 10_1101-2020_10_26_351783 67 8 Beta- Beta- NNP 10_1101-2020_10_26_351783 67 9 Mixture Mixture NNP 10_1101-2020_10_26_351783 67 10 Quantile Quantile NNP 10_1101-2020_10_26_351783 67 11 dilation dilation NN 10_1101-2020_10_26_351783 67 12 ( ( -LRB- 10_1101-2020_10_26_351783 67 13 BMIQ BMIQ NNP 10_1101-2020_10_26_351783 67 14 ) ) -RRB- 10_1101-2020_10_26_351783 67 15 normalization normalization NN 10_1101-2020_10_26_351783 67 16 method[15 method[15 NNP 10_1101-2020_10_26_351783 67 17 ] ] -RRB- 10_1101-2020_10_26_351783 67 18 � � NNP 10_1101-2020_10_26_351783 67 19 , , , 10_1101-2020_10_26_351783 67 20 including include VBG 10_1101-2020_10_26_351783 67 21 correction correction NN 10_1101-2020_10_26_351783 67 22 of of IN 10_1101-2020_10_26_351783 67 23 Type type NN 10_1101-2020_10_26_351783 67 24 - - HYPH 10_1101-2020_10_26_351783 67 25 I I NNP 10_1101-2020_10_26_351783 67 26 and and CC 10_1101-2020_10_26_351783 67 27 Type Type NNP 10_1101-2020_10_26_351783 67 28 - - HYPH 10_1101-2020_10_26_351783 67 29 II II NNP 10_1101-2020_10_26_351783 67 30 probe probe NN 10_1101-2020_10_26_351783 67 31 effects effect NNS 10_1101-2020_10_26_351783 67 32 . . . 10_1101-2020_10_26_351783 68 1 Data datum NNS 10_1101-2020_10_26_351783 68 2 quality quality NN 10_1101-2020_10_26_351783 68 3 was be VBD 10_1101-2020_10_26_351783 68 4 assessed assess VBN 10_1101-2020_10_26_351783 68 5 by by IN 10_1101-2020_10_26_351783 68 6 producing produce VBG 10_1101-2020_10_26_351783 68 7 multi multi JJ 10_1101-2020_10_26_351783 68 8 - - JJ 10_1101-2020_10_26_351783 68 9 dimensional dimensional JJ 10_1101-2020_10_26_351783 68 10 scaling scaling NN 10_1101-2020_10_26_351783 68 11 ( ( -LRB- 10_1101-2020_10_26_351783 68 12 MDS MDS NNP 10_1101-2020_10_26_351783 68 13 ) ) -RRB- 10_1101-2020_10_26_351783 68 14 plots plot NNS 10_1101-2020_10_26_351783 68 15 of of IN 10_1101-2020_10_26_351783 68 16 the the DT 10_1101-2020_10_26_351783 68 17 top top JJ 10_1101-2020_10_26_351783 68 18 1,000 1,000 CD 10_1101-2020_10_26_351783 68 19 most most RBS 10_1101-2020_10_26_351783 68 20 variable variable JJ 10_1101-2020_10_26_351783 68 21 positions position NNS 10_1101-2020_10_26_351783 68 22 per per IN 10_1101-2020_10_26_351783 68 23 sample sample NN 10_1101-2020_10_26_351783 68 24 , , , 10_1101-2020_10_26_351783 68 25 density density NN 10_1101-2020_10_26_351783 68 26 plots plot NNS 10_1101-2020_10_26_351783 68 27 for for IN 10_1101-2020_10_26_351783 68 28 the the DT 10_1101-2020_10_26_351783 68 29 distribution distribution NN 10_1101-2020_10_26_351783 68 30 of of IN 10_1101-2020_10_26_351783 68 31 beta beta JJ 10_1101-2020_10_26_351783 68 32 values value NNS 10_1101-2020_10_26_351783 68 33 , , , 10_1101-2020_10_26_351783 68 34 and and CC 10_1101-2020_10_26_351783 68 35 hierarchical hierarchical NN 10_1101-2020_10_26_351783 68 36 clustering clustering NN 10_1101-2020_10_26_351783 68 37 of of IN 10_1101-2020_10_26_351783 68 38 samples sample NNS 10_1101-2020_10_26_351783 68 39 , , , 10_1101-2020_10_26_351783 68 40 before before RB 10_1101-2020_10_26_351783 68 41 and and CC 10_1101-2020_10_26_351783 68 42 after after IN 10_1101-2020_10_26_351783 68 43 normalization normalization NN 10_1101-2020_10_26_351783 68 44 . . . 10_1101-2020_10_26_351783 69 1 Singular singular JJ 10_1101-2020_10_26_351783 69 2 value value NN 10_1101-2020_10_26_351783 69 3 decomposition decomposition NN 10_1101-2020_10_26_351783 69 4 ( ( -LRB- 10_1101-2020_10_26_351783 69 5 SVD SVD NNP 10_1101-2020_10_26_351783 69 6 ) ) -RRB- 10_1101-2020_10_26_351783 69 7 was be VBD 10_1101-2020_10_26_351783 69 8 used use VBN 10_1101-2020_10_26_351783 69 9 to to TO 10_1101-2020_10_26_351783 69 10 detect detect VB 10_1101-2020_10_26_351783 69 11 the the DT 10_1101-2020_10_26_351783 69 12 most most RBS 10_1101-2020_10_26_351783 69 13 significant significant JJ 10_1101-2020_10_26_351783 69 14 components component NNS 10_1101-2020_10_26_351783 69 15 of of IN 10_1101-2020_10_26_351783 69 16 variation variation NN 10_1101-2020_10_26_351783 69 17 in in IN 10_1101-2020_10_26_351783 69 18 the the DT 10_1101-2020_10_26_351783 69 19 data datum NNS 10_1101-2020_10_26_351783 69 20 . . . 10_1101-2020_10_26_351783 70 1 Unwanted unwanted JJ 10_1101-2020_10_26_351783 70 2 sources source NNS 10_1101-2020_10_26_351783 70 3 of of IN 10_1101-2020_10_26_351783 70 4 variation variation NN 10_1101-2020_10_26_351783 70 5 in in IN 10_1101-2020_10_26_351783 70 6 the the DT 10_1101-2020_10_26_351783 70 7 normalized normalized JJ 10_1101-2020_10_26_351783 70 8 data datum NNS 10_1101-2020_10_26_351783 70 9 were be VBD 10_1101-2020_10_26_351783 70 10 corrected correct VBN 10_1101-2020_10_26_351783 70 11 using use VBG 10_1101-2020_10_26_351783 70 12 ComBat ComBat NNP 10_1101-2020_10_26_351783 70 13 batch batch NN 10_1101-2020_10_26_351783 70 14 effect effect NN 10_1101-2020_10_26_351783 70 15 correction[16 correction[16 NNP 10_1101-2020_10_26_351783 70 16 ] ] -RRB- 10_1101-2020_10_26_351783 70 17 . . . 10_1101-2020_10_26_351783 71 1 Module module JJ 10_1101-2020_10_26_351783 71 2 Identification identification NN 10_1101-2020_10_26_351783 71 3 The the DT 10_1101-2020_10_26_351783 71 4 MODifieR13 modifier13 NN 10_1101-2020_10_26_351783 71 5 R r NN 10_1101-2020_10_26_351783 71 6 package package NN 10_1101-2020_10_26_351783 71 7 offers offer VBZ 10_1101-2020_10_26_351783 71 8 nine nine CD 10_1101-2020_10_26_351783 71 9 different different JJ 10_1101-2020_10_26_351783 71 10 methods method NNS 10_1101-2020_10_26_351783 71 11 for for IN 10_1101-2020_10_26_351783 71 12 producing produce VBG 10_1101-2020_10_26_351783 71 13 disease disease NN 10_1101-2020_10_26_351783 71 14 modules module NNS 10_1101-2020_10_26_351783 71 15 for for IN 10_1101-2020_10_26_351783 71 16 which which WDT 10_1101-2020_10_26_351783 71 17 we -PRON- PRP 10_1101-2020_10_26_351783 71 18 included include VBD 10_1101-2020_10_26_351783 71 19 all all DT 10_1101-2020_10_26_351783 71 20 but but CC 10_1101-2020_10_26_351783 71 21 Clique Clique NNP 10_1101-2020_10_26_351783 71 22 SuM sum NN 10_1101-2020_10_26_351783 71 23 exact exact JJ 10_1101-2020_10_26_351783 71 24 as as IN 10_1101-2020_10_26_351783 71 25 it -PRON- PRP 10_1101-2020_10_26_351783 71 26 is be VBZ 10_1101-2020_10_26_351783 71 27 highly highly RB 10_1101-2020_10_26_351783 71 28 similar similar JJ 10_1101-2020_10_26_351783 71 29 to to IN 10_1101-2020_10_26_351783 71 30 Clique Clique NNP 10_1101-2020_10_26_351783 71 31 SuM. SuM. NNP 10_1101-2020_10_26_351783 72 1 The the DT 10_1101-2020_10_26_351783 72 2 included include VBN 10_1101-2020_10_26_351783 72 3 methods method NNS 10_1101-2020_10_26_351783 72 4 will will MD 10_1101-2020_10_26_351783 72 5 produce produce VB 10_1101-2020_10_26_351783 72 6 modules module NNS 10_1101-2020_10_26_351783 72 7 based base VBN 10_1101-2020_10_26_351783 72 8 on on IN 10_1101-2020_10_26_351783 72 9 the the DT 10_1101-2020_10_26_351783 72 10 provided provide VBN 10_1101-2020_10_26_351783 72 11 omics omic NNS 10_1101-2020_10_26_351783 72 12 input input NN 10_1101-2020_10_26_351783 72 13 and and CC 10_1101-2020_10_26_351783 72 14 background background NN 10_1101-2020_10_26_351783 72 15 network network NN 10_1101-2020_10_26_351783 72 16 and and CC 10_1101-2020_10_26_351783 72 17 do do VBP 10_1101-2020_10_26_351783 72 18 not not RB 10_1101-2020_10_26_351783 72 19 include include VB 10_1101-2020_10_26_351783 72 20 prioritization prioritization NN 10_1101-2020_10_26_351783 72 21 of of IN 10_1101-2020_10_26_351783 72 22 pathway pathway NNP 10_1101-2020_10_26_351783 72 23 association association NNP 10_1101-2020_10_26_351783 72 24 . . . 10_1101-2020_10_26_351783 73 1 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 73 2 methods method NNS 10_1101-2020_10_26_351783 73 3 used use VBN 10_1101-2020_10_26_351783 73 4 for for IN 10_1101-2020_10_26_351783 73 5 module module JJ 10_1101-2020_10_26_351783 73 6 identification identification NN 10_1101-2020_10_26_351783 73 7 through through IN 10_1101-2020_10_26_351783 73 8 this this DT 10_1101-2020_10_26_351783 73 9 study study NN 10_1101-2020_10_26_351783 73 10 are be VBP 10_1101-2020_10_26_351783 73 11 listed list VBN 10_1101-2020_10_26_351783 73 12 in in IN 10_1101-2020_10_26_351783 73 13 the the DT 10_1101-2020_10_26_351783 73 14 Supplementary Supplementary NNP 10_1101-2020_10_26_351783 73 15 Table Table NNP 10_1101-2020_10_26_351783 73 16 3 3 CD 10_1101-2020_10_26_351783 73 17 . . . 10_1101-2020_10_26_351783 74 1 For for IN 10_1101-2020_10_26_351783 74 2 the the DT 10_1101-2020_10_26_351783 74 3 methods method NNS 10_1101-2020_10_26_351783 74 4 that that WDT 10_1101-2020_10_26_351783 74 5 require require VBP 10_1101-2020_10_26_351783 74 6 a a DT 10_1101-2020_10_26_351783 74 7 network network NN 10_1101-2020_10_26_351783 74 8 , , , 10_1101-2020_10_26_351783 74 9 we -PRON- PRP 10_1101-2020_10_26_351783 74 10 used use VBD 10_1101-2020_10_26_351783 74 11 the the DT 10_1101-2020_10_26_351783 74 12 ( ( -LRB- 10_1101-2020_10_26_351783 74 13 which which WDT 10_1101-2020_10_26_351783 74 14 was be VBD 10_1101-2020_10_26_351783 74 15 not not RB 10_1101-2020_10_26_351783 74 16 certified certify VBN 10_1101-2020_10_26_351783 74 17 by by IN 10_1101-2020_10_26_351783 74 18 peer peer NN 10_1101-2020_10_26_351783 74 19 review review NN 10_1101-2020_10_26_351783 74 20 ) ) -RRB- 10_1101-2020_10_26_351783 74 21 is be VBZ 10_1101-2020_10_26_351783 74 22 the the DT 10_1101-2020_10_26_351783 74 23 author author NN 10_1101-2020_10_26_351783 74 24 / / SYM 10_1101-2020_10_26_351783 74 25 funder funder NN 10_1101-2020_10_26_351783 74 26 . . . 10_1101-2020_10_26_351783 75 1 All all DT 10_1101-2020_10_26_351783 75 2 rights right NNS 10_1101-2020_10_26_351783 75 3 reserved reserve VBD 10_1101-2020_10_26_351783 75 4 . . . 10_1101-2020_10_26_351783 76 1 No no DT 10_1101-2020_10_26_351783 76 2 reuse reuse NN 10_1101-2020_10_26_351783 76 3 allowed allow VBN 10_1101-2020_10_26_351783 76 4 without without IN 10_1101-2020_10_26_351783 76 5 permission permission NN 10_1101-2020_10_26_351783 76 6 . . . 10_1101-2020_10_26_351783 77 1 The the DT 10_1101-2020_10_26_351783 77 2 copyright copyright NN 10_1101-2020_10_26_351783 77 3 holder holder NN 10_1101-2020_10_26_351783 77 4 for for IN 10_1101-2020_10_26_351783 77 5 this this DT 10_1101-2020_10_26_351783 77 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 77 7 version version NN 10_1101-2020_10_26_351783 77 8 posted post VBD 10_1101-2020_10_26_351783 77 9 January January NNP 10_1101-2020_10_26_351783 77 10 6 6 CD 10_1101-2020_10_26_351783 77 11 , , , 10_1101-2020_10_26_351783 77 12 2021 2021 CD 10_1101-2020_10_26_351783 77 13 . . . 10_1101-2020_10_26_351783 77 14 ; ; : 10_1101-2020_10_26_351783 77 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 77 16 : : : 10_1101-2020_10_26_351783 77 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 77 18 preprint preprint NN 10_1101-2020_10_26_351783 77 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 77 20 7 7 CD 10_1101-2020_10_26_351783 77 21 human human JJ 10_1101-2020_10_26_351783 77 22 PPI PPI NNP 10_1101-2020_10_26_351783 77 23 network network NN 10_1101-2020_10_26_351783 77 24 from from IN 10_1101-2020_10_26_351783 77 25 STRING5 STRING5 NNP 10_1101-2020_10_26_351783 77 26 database database NNP 10_1101-2020_10_26_351783 77 27 version version NNP 10_1101-2020_10_26_351783 77 28 11 11 CD 10_1101-2020_10_26_351783 77 29 , , , 10_1101-2020_10_26_351783 77 30 consisting consist VBG 10_1101-2020_10_26_351783 77 31 of of IN 10_1101-2020_10_26_351783 77 32 11,295,036 11,295,036 CD 10_1101-2020_10_26_351783 77 33 interactions interaction NNS 10_1101-2020_10_26_351783 77 34 among among IN 10_1101-2020_10_26_351783 77 35 18,746 18,746 CD 10_1101-2020_10_26_351783 77 36 unique unique JJ 10_1101-2020_10_26_351783 77 37 genes gene NNS 10_1101-2020_10_26_351783 77 38 / / SYM 10_1101-2020_10_26_351783 77 39 proteins protein NNS 10_1101-2020_10_26_351783 77 40 . . . 10_1101-2020_10_26_351783 78 1 We -PRON- PRP 10_1101-2020_10_26_351783 78 2 filtered filter VBD 10_1101-2020_10_26_351783 78 3 the the DT 10_1101-2020_10_26_351783 78 4 network network NN 10_1101-2020_10_26_351783 78 5 to to TO 10_1101-2020_10_26_351783 78 6 have have VB 10_1101-2020_10_26_351783 78 7 high high JJ 10_1101-2020_10_26_351783 78 8 confidence confidence NN 10_1101-2020_10_26_351783 78 9 interactions interaction NNS 10_1101-2020_10_26_351783 78 10 by by IN 10_1101-2020_10_26_351783 78 11 using use VBG 10_1101-2020_10_26_351783 78 12 the the DT 10_1101-2020_10_26_351783 78 13 cutoff cutoff NN 10_1101-2020_10_26_351783 78 14 > > XX 10_1101-2020_10_26_351783 78 15 900 900 CD 10_1101-2020_10_26_351783 78 16 to to TO 10_1101-2020_10_26_351783 78 17 reduce reduce VB 10_1101-2020_10_26_351783 78 18 the the DT 10_1101-2020_10_26_351783 78 19 number number NN 10_1101-2020_10_26_351783 78 20 of of IN 10_1101-2020_10_26_351783 78 21 false false JJ 10_1101-2020_10_26_351783 78 22 positives positive NNS 10_1101-2020_10_26_351783 78 23 , , , 10_1101-2020_10_26_351783 78 24 resulting result VBG 10_1101-2020_10_26_351783 78 25 in in IN 10_1101-2020_10_26_351783 78 26 a a DT 10_1101-2020_10_26_351783 78 27 subset subset NN 10_1101-2020_10_26_351783 78 28 of of IN 10_1101-2020_10_26_351783 78 29 631,782 631,782 CD 10_1101-2020_10_26_351783 78 30 interactions interaction NNS 10_1101-2020_10_26_351783 78 31 between between IN 10_1101-2020_10_26_351783 78 32 12,123 12,123 CD 10_1101-2020_10_26_351783 78 33 unique unique JJ 10_1101-2020_10_26_351783 78 34 genes gene NNS 10_1101-2020_10_26_351783 78 35 / / SYM 10_1101-2020_10_26_351783 78 36 proteins protein NNS 10_1101-2020_10_26_351783 78 37 . . . 10_1101-2020_10_26_351783 79 1 For for IN 10_1101-2020_10_26_351783 79 2 co co JJ 10_1101-2020_10_26_351783 79 3 - - JJ 10_1101-2020_10_26_351783 79 4 expression expression JJ 10_1101-2020_10_26_351783 79 5 methods method NNS 10_1101-2020_10_26_351783 79 6 , , , 10_1101-2020_10_26_351783 79 7 the the DT 10_1101-2020_10_26_351783 79 8 network network NN 10_1101-2020_10_26_351783 79 9 is be VBZ 10_1101-2020_10_26_351783 79 10 computed compute VBN 10_1101-2020_10_26_351783 79 11 within within IN 10_1101-2020_10_26_351783 79 12 the the DT 10_1101-2020_10_26_351783 79 13 method method NN 10_1101-2020_10_26_351783 79 14 algorithm algorithm NN 10_1101-2020_10_26_351783 79 15 from from IN 10_1101-2020_10_26_351783 79 16 the the DT 10_1101-2020_10_26_351783 79 17 gene gene NN 10_1101-2020_10_26_351783 79 18 expression expression NN 10_1101-2020_10_26_351783 79 19 matrix matrix NNP 10_1101-2020_10_26_351783 79 20 . . . 10_1101-2020_10_26_351783 80 1 In in IN 10_1101-2020_10_26_351783 80 2 case case NN 10_1101-2020_10_26_351783 80 3 of of IN 10_1101-2020_10_26_351783 80 4 the the DT 10_1101-2020_10_26_351783 80 5 benchmark benchmark JJ 10_1101-2020_10_26_351783 80 6 analysis analysis NN 10_1101-2020_10_26_351783 80 7 , , , 10_1101-2020_10_26_351783 80 8 we -PRON- PRP 10_1101-2020_10_26_351783 80 9 used use VBD 10_1101-2020_10_26_351783 80 10 a a DT 10_1101-2020_10_26_351783 80 11 stringent stringent JJ 10_1101-2020_10_26_351783 80 12 cutoff cutoff NN 10_1101-2020_10_26_351783 80 13 of of IN 10_1101-2020_10_26_351783 80 14 score score NN 10_1101-2020_10_26_351783 80 15 > > XX 10_1101-2020_10_26_351783 80 16 900 900 CD 10_1101-2020_10_26_351783 80 17 , , , 10_1101-2020_10_26_351783 80 18 so so IN 10_1101-2020_10_26_351783 80 19 that that IN 10_1101-2020_10_26_351783 80 20 the the DT 10_1101-2020_10_26_351783 80 21 runs run NNS 10_1101-2020_10_26_351783 80 22 were be VBD 10_1101-2020_10_26_351783 80 23 not not RB 10_1101-2020_10_26_351783 80 24 computationally computationally RB 10_1101-2020_10_26_351783 80 25 intensive intensive JJ 10_1101-2020_10_26_351783 80 26 . . . 10_1101-2020_10_26_351783 81 1 For for IN 10_1101-2020_10_26_351783 81 2 the the DT 10_1101-2020_10_26_351783 81 3 MS MS NNP 10_1101-2020_10_26_351783 81 4 use use NN 10_1101-2020_10_26_351783 81 5 case case NN 10_1101-2020_10_26_351783 81 6 benchmark benchmark NN 10_1101-2020_10_26_351783 81 7 , , , 10_1101-2020_10_26_351783 81 8 we -PRON- PRP 10_1101-2020_10_26_351783 81 9 used use VBD 10_1101-2020_10_26_351783 81 10 the the DT 10_1101-2020_10_26_351783 81 11 network network NN 10_1101-2020_10_26_351783 81 12 combined combine VBN 10_1101-2020_10_26_351783 81 13 score score NN 10_1101-2020_10_26_351783 81 14 cutoff cutoff RB 10_1101-2020_10_26_351783 81 15 > > XX 10_1101-2020_10_26_351783 81 16 700 700 CD 10_1101-2020_10_26_351783 81 17 . . . 10_1101-2020_10_26_351783 82 1 The the DT 10_1101-2020_10_26_351783 82 2 processed processed JJ 10_1101-2020_10_26_351783 82 3 matrix matrix NN 10_1101-2020_10_26_351783 82 4 for for IN 10_1101-2020_10_26_351783 82 5 each each DT 10_1101-2020_10_26_351783 82 6 dataset dataset NN 10_1101-2020_10_26_351783 82 7 and and CC 10_1101-2020_10_26_351783 82 8 their -PRON- PRP$ 10_1101-2020_10_26_351783 82 9 respective respective JJ 10_1101-2020_10_26_351783 82 10 phenotypic phenotypic JJ 10_1101-2020_10_26_351783 82 11 information information NN 10_1101-2020_10_26_351783 82 12 were be VBD 10_1101-2020_10_26_351783 82 13 downloaded download VBN 10_1101-2020_10_26_351783 82 14 from from IN 10_1101-2020_10_26_351783 82 15 GEO GEO NNP 10_1101-2020_10_26_351783 82 16 . . . 10_1101-2020_10_26_351783 83 1 The the DT 10_1101-2020_10_26_351783 83 2 input input NN 10_1101-2020_10_26_351783 83 3 object object NN 10_1101-2020_10_26_351783 83 4 is be VBZ 10_1101-2020_10_26_351783 83 5 prepared prepare VBN 10_1101-2020_10_26_351783 83 6 using use VBG 10_1101-2020_10_26_351783 83 7 the the DT 10_1101-2020_10_26_351783 83 8 create_input_microarray create_input_microarray NN 10_1101-2020_10_26_351783 83 9 function function NN 10_1101-2020_10_26_351783 83 10 from from IN 10_1101-2020_10_26_351783 83 11 the the DT 10_1101-2020_10_26_351783 83 12 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 83 13 package package NN 10_1101-2020_10_26_351783 83 14 which which WDT 10_1101-2020_10_26_351783 83 15 is be VBZ 10_1101-2020_10_26_351783 83 16 then then RB 10_1101-2020_10_26_351783 83 17 used use VBN 10_1101-2020_10_26_351783 83 18 for for IN 10_1101-2020_10_26_351783 83 19 creating create VBG 10_1101-2020_10_26_351783 83 20 the the DT 10_1101-2020_10_26_351783 83 21 modules module NNS 10_1101-2020_10_26_351783 83 22 . . . 10_1101-2020_10_26_351783 84 1 The the DT 10_1101-2020_10_26_351783 84 2 input input NN 10_1101-2020_10_26_351783 84 3 function function NN 10_1101-2020_10_26_351783 84 4 applies apply VBZ 10_1101-2020_10_26_351783 84 5 linear linear JJ 10_1101-2020_10_26_351783 84 6 model model NN 10_1101-2020_10_26_351783 84 7 using use VBG 10_1101-2020_10_26_351783 84 8 limma limma NN 10_1101-2020_10_26_351783 84 9 for for IN 10_1101-2020_10_26_351783 84 10 comparison comparison NN 10_1101-2020_10_26_351783 84 11 of of IN 10_1101-2020_10_26_351783 84 12 patient patient NNP 10_1101-2020_10_26_351783 84 13 's 's POS 10_1101-2020_10_26_351783 84 14 vs vs NNP 10_1101-2020_10_26_351783 84 15 controls control NNS 10_1101-2020_10_26_351783 84 16 to to TO 10_1101-2020_10_26_351783 84 17 get get VB 10_1101-2020_10_26_351783 84 18 the the DT 10_1101-2020_10_26_351783 84 19 differentially differentially RB 10_1101-2020_10_26_351783 84 20 methylated methylate VBN 10_1101-2020_10_26_351783 84 21 or or CC 10_1101-2020_10_26_351783 84 22 expressed express VBN 10_1101-2020_10_26_351783 84 23 genes gene NNS 10_1101-2020_10_26_351783 84 24 . . . 10_1101-2020_10_26_351783 85 1 A a DT 10_1101-2020_10_26_351783 85 2 dynamic dynamic JJ 10_1101-2020_10_26_351783 85 3 cutoff cutoff NN 10_1101-2020_10_26_351783 85 4 of of IN 10_1101-2020_10_26_351783 85 5 5 5 CD 10_1101-2020_10_26_351783 85 6 % % NN 10_1101-2020_10_26_351783 85 7 in in IN 10_1101-2020_10_26_351783 85 8 the the DT 10_1101-2020_10_26_351783 85 9 differentially differentially RB 10_1101-2020_10_26_351783 85 10 methylated methylate VBN 10_1101-2020_10_26_351783 85 11 or or CC 10_1101-2020_10_26_351783 85 12 expressed express VBN 10_1101-2020_10_26_351783 85 13 genes gene NNS 10_1101-2020_10_26_351783 85 14 is be VBZ 10_1101-2020_10_26_351783 85 15 applied apply VBN 10_1101-2020_10_26_351783 85 16 for for IN 10_1101-2020_10_26_351783 85 17 input input NN 10_1101-2020_10_26_351783 85 18 seed seed NN 10_1101-2020_10_26_351783 85 19 genes gene NNS 10_1101-2020_10_26_351783 85 20 for for IN 10_1101-2020_10_26_351783 85 21 the the DT 10_1101-2020_10_26_351783 85 22 methods method NNS 10_1101-2020_10_26_351783 85 23 that that WDT 10_1101-2020_10_26_351783 85 24 require require VBP 10_1101-2020_10_26_351783 85 25 seed seed NN 10_1101-2020_10_26_351783 85 26 genes gene NNS 10_1101-2020_10_26_351783 85 27 . . . 10_1101-2020_10_26_351783 86 1 Differential differential NN 10_1101-2020_10_26_351783 86 2 methylation methylation NN 10_1101-2020_10_26_351783 86 3 analysis analysis NN 10_1101-2020_10_26_351783 86 4 of of IN 10_1101-2020_10_26_351783 86 5 risk risk NN 10_1101-2020_10_26_351783 86 6 factor factor NN 10_1101-2020_10_26_351783 86 7 data datum NNS 10_1101-2020_10_26_351783 86 8 Differentially differentially RB 10_1101-2020_10_26_351783 86 9 methylated methylate VBD 10_1101-2020_10_26_351783 86 10 probes probe NNS 10_1101-2020_10_26_351783 86 11 ( ( -LRB- 10_1101-2020_10_26_351783 86 12 DMPs DMPs NNP 10_1101-2020_10_26_351783 86 13 ) ) -RRB- 10_1101-2020_10_26_351783 86 14 were be VBD 10_1101-2020_10_26_351783 86 15 found find VBN 10_1101-2020_10_26_351783 86 16 by by IN 10_1101-2020_10_26_351783 86 17 fitting fit VBG 10_1101-2020_10_26_351783 86 18 a a DT 10_1101-2020_10_26_351783 86 19 linear linear JJ 10_1101-2020_10_26_351783 86 20 model model NN 10_1101-2020_10_26_351783 86 21 to to IN 10_1101-2020_10_26_351783 86 22 the the DT 10_1101-2020_10_26_351783 86 23 data datum NNS 10_1101-2020_10_26_351783 86 24 using use VBG 10_1101-2020_10_26_351783 86 25 the the DT 10_1101-2020_10_26_351783 86 26 limma limma NN 10_1101-2020_10_26_351783 86 27 R R NNP 10_1101-2020_10_26_351783 86 28 package[17 package[17 NNP 10_1101-2020_10_26_351783 86 29 ] ] -RRB- 10_1101-2020_10_26_351783 86 30 � � NNP 10_1101-2020_10_26_351783 86 31 , , , 10_1101-2020_10_26_351783 86 32 version version NN 10_1101-2020_10_26_351783 86 33 3.42.2 3.42.2 CD 10_1101-2020_10_26_351783 86 34 implemented implement VBN 10_1101-2020_10_26_351783 86 35 in in IN 10_1101-2020_10_26_351783 86 36 the the DT 10_1101-2020_10_26_351783 86 37 ChAMP ChAMP NNP 10_1101-2020_10_26_351783 86 38 function function NN 10_1101-2020_10_26_351783 86 39 champ champ NN 10_1101-2020_10_26_351783 86 40 . . . 10_1101-2020_10_26_351783 86 41 DMP DMP NNP 10_1101-2020_10_26_351783 86 42 . . . 10_1101-2020_10_26_351783 87 1 P p NN 10_1101-2020_10_26_351783 87 2 - - HYPH 10_1101-2020_10_26_351783 87 3 values value NNS 10_1101-2020_10_26_351783 87 4 were be VBD 10_1101-2020_10_26_351783 87 5 adjusted adjust VBN 10_1101-2020_10_26_351783 87 6 for for IN 10_1101-2020_10_26_351783 87 7 multiple multiple JJ 10_1101-2020_10_26_351783 87 8 testing testing NN 10_1101-2020_10_26_351783 87 9 using use VBG 10_1101-2020_10_26_351783 87 10 Benjamini Benjamini NNP 10_1101-2020_10_26_351783 87 11 - - HYPH 10_1101-2020_10_26_351783 87 12 Hochberg Hochberg NNP 10_1101-2020_10_26_351783 87 13 False False NNP 10_1101-2020_10_26_351783 87 14 Discovery Discovery NNP 10_1101-2020_10_26_351783 87 15 Rate Rate NNP 10_1101-2020_10_26_351783 87 16 ( ( -LRB- 10_1101-2020_10_26_351783 87 17 FDR FDR NNP 10_1101-2020_10_26_351783 87 18 ) ) -RRB- 10_1101-2020_10_26_351783 87 19 correction correction NN 10_1101-2020_10_26_351783 87 20 . . . 10_1101-2020_10_26_351783 88 1 Differentially differentially RB 10_1101-2020_10_26_351783 88 2 methylated methylate VBN 10_1101-2020_10_26_351783 88 3 genes gene NNS 10_1101-2020_10_26_351783 88 4 ( ( -LRB- 10_1101-2020_10_26_351783 88 5 DMGs DMGs NNP 10_1101-2020_10_26_351783 88 6 ) ) -RRB- 10_1101-2020_10_26_351783 88 7 were be VBD 10_1101-2020_10_26_351783 88 8 obtained obtain VBN 10_1101-2020_10_26_351783 88 9 and and CC 10_1101-2020_10_26_351783 88 10 annotated annotate VBN 10_1101-2020_10_26_351783 88 11 using use VBG 10_1101-2020_10_26_351783 88 12 the the DT 10_1101-2020_10_26_351783 88 13 org.Hs.eg.db org.Hs.eg.db NNP 10_1101-2020_10_26_351783 88 14 R r NN 10_1101-2020_10_26_351783 88 15 package package NN 10_1101-2020_10_26_351783 88 16 � � NNP 10_1101-2020_10_26_351783 88 17 , , , 10_1101-2020_10_26_351783 88 18 version version NN 10_1101-2020_10_26_351783 88 19 3.10.0 3.10.0 CD 10_1101-2020_10_26_351783 88 20 . . . 10_1101-2020_10_26_351783 89 1 DMG DMG NNP 10_1101-2020_10_26_351783 89 2 lists list NNS 10_1101-2020_10_26_351783 89 3 were be VBD 10_1101-2020_10_26_351783 89 4 cross cross JJ 10_1101-2020_10_26_351783 89 5 - - VBN 10_1101-2020_10_26_351783 89 6 checked check VBN 10_1101-2020_10_26_351783 89 7 against against IN 10_1101-2020_10_26_351783 89 8 the the DT 10_1101-2020_10_26_351783 89 9 STRING string NN 10_1101-2020_10_26_351783 89 10 database database NN 10_1101-2020_10_26_351783 89 11 version version NN 10_1101-2020_10_26_351783 89 12 11 11 CD 10_1101-2020_10_26_351783 89 13 PPI PPI NNP 10_1101-2020_10_26_351783 89 14 network network NN 10_1101-2020_10_26_351783 89 15 used use VBN 10_1101-2020_10_26_351783 89 16 for for IN 10_1101-2020_10_26_351783 89 17 module module JJ 10_1101-2020_10_26_351783 89 18 identification identification NN 10_1101-2020_10_26_351783 89 19 in in IN 10_1101-2020_10_26_351783 89 20 the the DT 10_1101-2020_10_26_351783 89 21 MS MS NNP 10_1101-2020_10_26_351783 89 22 multi multi JJ 10_1101-2020_10_26_351783 89 23 - - HYPH 10_1101-2020_10_26_351783 89 24 omics omics JJ 10_1101-2020_10_26_351783 89 25 approach approach NN 10_1101-2020_10_26_351783 89 26 ( ( -LRB- 10_1101-2020_10_26_351783 89 27 high high JJ 10_1101-2020_10_26_351783 89 28 confidence confidence NN 10_1101-2020_10_26_351783 89 29 interactions interaction NNS 10_1101-2020_10_26_351783 89 30 , , , 10_1101-2020_10_26_351783 89 31 combined combine VBN 10_1101-2020_10_26_351783 89 32 score score NN 10_1101-2020_10_26_351783 89 33 > > XX 10_1101-2020_10_26_351783 89 34 700 700 CD 10_1101-2020_10_26_351783 89 35 ) ) -RRB- 10_1101-2020_10_26_351783 89 36 . . . 10_1101-2020_10_26_351783 90 1 DMGs dmg NNS 10_1101-2020_10_26_351783 90 2 that that WDT 10_1101-2020_10_26_351783 90 3 were be VBD 10_1101-2020_10_26_351783 90 4 not not RB 10_1101-2020_10_26_351783 90 5 present present JJ 10_1101-2020_10_26_351783 90 6 in in IN 10_1101-2020_10_26_351783 90 7 the the DT 10_1101-2020_10_26_351783 90 8 PPI PPI NNP 10_1101-2020_10_26_351783 90 9 network network NN 10_1101-2020_10_26_351783 90 10 were be VBD 10_1101-2020_10_26_351783 90 11 removed remove VBN 10_1101-2020_10_26_351783 90 12 . . . 10_1101-2020_10_26_351783 91 1 In in IN 10_1101-2020_10_26_351783 91 2 case case NN 10_1101-2020_10_26_351783 91 3 of of IN 10_1101-2020_10_26_351783 91 4 the the DT 10_1101-2020_10_26_351783 91 5 additional additional JJ 10_1101-2020_10_26_351783 91 6 MS MS NNP 10_1101-2020_10_26_351783 91 7 validation validation NN 10_1101-2020_10_26_351783 91 8 dataset dataset NN 10_1101-2020_10_26_351783 91 9 , , , 10_1101-2020_10_26_351783 91 10 a a DT 10_1101-2020_10_26_351783 91 11 linear linear JJ 10_1101-2020_10_26_351783 91 12 mixed mixed JJ 10_1101-2020_10_26_351783 91 13 effect effect NN 10_1101-2020_10_26_351783 91 14 model model NN 10_1101-2020_10_26_351783 91 15 with with IN 10_1101-2020_10_26_351783 91 16 risk risk NN 10_1101-2020_10_26_351783 91 17 factors factor NNS 10_1101-2020_10_26_351783 91 18 ( ( -LRB- 10_1101-2020_10_26_351783 91 19 age age NN 10_1101-2020_10_26_351783 91 20 , , , 10_1101-2020_10_26_351783 91 21 sex sex NN 10_1101-2020_10_26_351783 91 22 , , , 10_1101-2020_10_26_351783 91 23 BMI BMI NNP 10_1101-2020_10_26_351783 91 24 at at IN 10_1101-2020_10_26_351783 91 25 age age NN 10_1101-2020_10_26_351783 91 26 of of IN 10_1101-2020_10_26_351783 91 27 20 20 CD 10_1101-2020_10_26_351783 91 28 , , , 10_1101-2020_10_26_351783 91 29 smoking smoking NN 10_1101-2020_10_26_351783 91 30 , , , 10_1101-2020_10_26_351783 91 31 alcohol alcohol NN 10_1101-2020_10_26_351783 91 32 consumption consumption NN 10_1101-2020_10_26_351783 91 33 , , , 10_1101-2020_10_26_351783 91 34 sun sun NN 10_1101-2020_10_26_351783 91 35 exposure exposure NN 10_1101-2020_10_26_351783 91 36 , , , 10_1101-2020_10_26_351783 91 37 night night NN 10_1101-2020_10_26_351783 91 38 shift shift NN 10_1101-2020_10_26_351783 91 39 work work NN 10_1101-2020_10_26_351783 91 40 , , , 10_1101-2020_10_26_351783 91 41 contact contact NN 10_1101-2020_10_26_351783 91 42 with with IN 10_1101-2020_10_26_351783 91 43 organic organic JJ 10_1101-2020_10_26_351783 91 44 solvents solvent NNS 10_1101-2020_10_26_351783 91 45 ) ) -RRB- 10_1101-2020_10_26_351783 91 46 as as IN 10_1101-2020_10_26_351783 91 47 categorical categorical JJ 10_1101-2020_10_26_351783 91 48 covariates covariate NNS 10_1101-2020_10_26_351783 91 49 was be VBD 10_1101-2020_10_26_351783 91 50 implemented implement VBN 10_1101-2020_10_26_351783 91 51 to to TO 10_1101-2020_10_26_351783 91 52 find find VB 10_1101-2020_10_26_351783 91 53 the the DT 10_1101-2020_10_26_351783 91 54 differentially differentially RB 10_1101-2020_10_26_351783 91 55 methylated methylate VBN 10_1101-2020_10_26_351783 91 56 genes gene NNS 10_1101-2020_10_26_351783 91 57 after after IN 10_1101-2020_10_26_351783 91 58 the the DT 10_1101-2020_10_26_351783 91 59 preprocessing preprocessing NN 10_1101-2020_10_26_351783 91 60 step step NN 10_1101-2020_10_26_351783 91 61 , , , 10_1101-2020_10_26_351783 91 62 as as IN 10_1101-2020_10_26_351783 91 63 described describe VBN 10_1101-2020_10_26_351783 91 64 in in IN 10_1101-2020_10_26_351783 91 65 the the DT 10_1101-2020_10_26_351783 91 66 preprocessing preprocessing NN 10_1101-2020_10_26_351783 91 67 section section NN 10_1101-2020_10_26_351783 91 68 of of IN 10_1101-2020_10_26_351783 91 69 the the DT 10_1101-2020_10_26_351783 91 70 methods method NNS 10_1101-2020_10_26_351783 91 71 . . . 10_1101-2020_10_26_351783 92 1 Since since IN 10_1101-2020_10_26_351783 92 2 all all PDT 10_1101-2020_10_26_351783 92 3 the the DT 10_1101-2020_10_26_351783 92 4 patients patient NNS 10_1101-2020_10_26_351783 92 5 were be VBD 10_1101-2020_10_26_351783 92 6 EBV EBV NNP 10_1101-2020_10_26_351783 92 7 positive positive JJ 10_1101-2020_10_26_351783 92 8 , , , 10_1101-2020_10_26_351783 92 9 we -PRON- PRP 10_1101-2020_10_26_351783 92 10 did do VBD 10_1101-2020_10_26_351783 92 11 not not RB 10_1101-2020_10_26_351783 92 12 include include VB 10_1101-2020_10_26_351783 92 13 it -PRON- PRP 10_1101-2020_10_26_351783 92 14 for for IN 10_1101-2020_10_26_351783 92 15 linear linear JJ 10_1101-2020_10_26_351783 92 16 mixed mixed JJ 10_1101-2020_10_26_351783 92 17 effect effect NN 10_1101-2020_10_26_351783 92 18 model model NN 10_1101-2020_10_26_351783 92 19 . . . 10_1101-2020_10_26_351783 93 1 ( ( -LRB- 10_1101-2020_10_26_351783 93 2 which which WDT 10_1101-2020_10_26_351783 93 3 was be VBD 10_1101-2020_10_26_351783 93 4 not not RB 10_1101-2020_10_26_351783 93 5 certified certify VBN 10_1101-2020_10_26_351783 93 6 by by IN 10_1101-2020_10_26_351783 93 7 peer peer NN 10_1101-2020_10_26_351783 93 8 review review NN 10_1101-2020_10_26_351783 93 9 ) ) -RRB- 10_1101-2020_10_26_351783 93 10 is be VBZ 10_1101-2020_10_26_351783 93 11 the the DT 10_1101-2020_10_26_351783 93 12 author author NN 10_1101-2020_10_26_351783 93 13 / / SYM 10_1101-2020_10_26_351783 93 14 funder funder NN 10_1101-2020_10_26_351783 93 15 . . . 10_1101-2020_10_26_351783 94 1 All all DT 10_1101-2020_10_26_351783 94 2 rights right NNS 10_1101-2020_10_26_351783 94 3 reserved reserve VBD 10_1101-2020_10_26_351783 94 4 . . . 10_1101-2020_10_26_351783 95 1 No no DT 10_1101-2020_10_26_351783 95 2 reuse reuse NN 10_1101-2020_10_26_351783 95 3 allowed allow VBN 10_1101-2020_10_26_351783 95 4 without without IN 10_1101-2020_10_26_351783 95 5 permission permission NN 10_1101-2020_10_26_351783 95 6 . . . 10_1101-2020_10_26_351783 96 1 The the DT 10_1101-2020_10_26_351783 96 2 copyright copyright NN 10_1101-2020_10_26_351783 96 3 holder holder NN 10_1101-2020_10_26_351783 96 4 for for IN 10_1101-2020_10_26_351783 96 5 this this DT 10_1101-2020_10_26_351783 96 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 96 7 version version NN 10_1101-2020_10_26_351783 96 8 posted post VBD 10_1101-2020_10_26_351783 96 9 January January NNP 10_1101-2020_10_26_351783 96 10 6 6 CD 10_1101-2020_10_26_351783 96 11 , , , 10_1101-2020_10_26_351783 96 12 2021 2021 CD 10_1101-2020_10_26_351783 96 13 . . . 10_1101-2020_10_26_351783 96 14 ; ; : 10_1101-2020_10_26_351783 96 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 96 16 : : : 10_1101-2020_10_26_351783 96 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 96 18 preprint preprint NN 10_1101-2020_10_26_351783 96 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 96 20 8 8 CD 10_1101-2020_10_26_351783 96 21 Validation validation NN 10_1101-2020_10_26_351783 96 22 of of IN 10_1101-2020_10_26_351783 96 23 modules module NNS 10_1101-2020_10_26_351783 96 24 The the DT 10_1101-2020_10_26_351783 96 25 final final JJ 10_1101-2020_10_26_351783 96 26 modules module NNS 10_1101-2020_10_26_351783 96 27 produced produce VBN 10_1101-2020_10_26_351783 96 28 from from IN 10_1101-2020_10_26_351783 96 29 each each DT 10_1101-2020_10_26_351783 96 30 single single JJ 10_1101-2020_10_26_351783 96 31 algorithm algorithm NN 10_1101-2020_10_26_351783 96 32 and and CC 10_1101-2020_10_26_351783 96 33 the the DT 10_1101-2020_10_26_351783 96 34 consensus consensus NN 10_1101-2020_10_26_351783 96 35 were be VBD 10_1101-2020_10_26_351783 96 36 evaluated evaluate VBN 10_1101-2020_10_26_351783 96 37 using use VBG 10_1101-2020_10_26_351783 96 38 Pascal[18 pascal[18 ADD 10_1101-2020_10_26_351783 96 39 ] ] -RRB- 10_1101-2020_10_26_351783 96 40 ( ( -LRB- 10_1101-2020_10_26_351783 96 41 Pathway Pathway NNP 10_1101-2020_10_26_351783 96 42 scoring score VBG 10_1101-2020_10_26_351783 96 43 algorithm algorithm NN 10_1101-2020_10_26_351783 96 44 ) ) -RRB- 10_1101-2020_10_26_351783 96 45 . . . 10_1101-2020_10_26_351783 97 1 Pascal pascal JJ 10_1101-2020_10_26_351783 97 2 implements implement NNS 10_1101-2020_10_26_351783 97 3 a a DT 10_1101-2020_10_26_351783 97 4 fast fast JJ 10_1101-2020_10_26_351783 97 5 and and CC 10_1101-2020_10_26_351783 97 6 rigorous rigorous JJ 10_1101-2020_10_26_351783 97 7 gene gene NN 10_1101-2020_10_26_351783 97 8 scoring scoring NN 10_1101-2020_10_26_351783 97 9 and and CC 10_1101-2020_10_26_351783 97 10 pathway pathway JJ 10_1101-2020_10_26_351783 97 11 enrichment enrichment NN 10_1101-2020_10_26_351783 97 12 pipeline pipeline NN 10_1101-2020_10_26_351783 97 13 that that WDT 10_1101-2020_10_26_351783 97 14 can can MD 10_1101-2020_10_26_351783 97 15 be be VB 10_1101-2020_10_26_351783 97 16 run run VBN 10_1101-2020_10_26_351783 97 17 on on IN 10_1101-2020_10_26_351783 97 18 a a DT 10_1101-2020_10_26_351783 97 19 local local JJ 10_1101-2020_10_26_351783 97 20 machine machine NN 10_1101-2020_10_26_351783 97 21 . . . 10_1101-2020_10_26_351783 98 1 The the DT 10_1101-2020_10_26_351783 98 2 SNP SNP NNP 10_1101-2020_10_26_351783 98 3 values value NNS 10_1101-2020_10_26_351783 98 4 are be VBP 10_1101-2020_10_26_351783 98 5 converted convert VBN 10_1101-2020_10_26_351783 98 6 to to IN 10_1101-2020_10_26_351783 98 7 gene gene NN 10_1101-2020_10_26_351783 98 8 scores score NNS 10_1101-2020_10_26_351783 98 9 by by IN 10_1101-2020_10_26_351783 98 10 computing compute VBG 10_1101-2020_10_26_351783 98 11 pairwise pairwise NN 10_1101-2020_10_26_351783 98 12 SNP SNP NNP 10_1101-2020_10_26_351783 98 13 - - HYPH 10_1101-2020_10_26_351783 98 14 by by IN 10_1101-2020_10_26_351783 98 15 - - HYPH 10_1101-2020_10_26_351783 98 16 SNP SNP NNP 10_1101-2020_10_26_351783 98 17 correlations correlation NNS 10_1101-2020_10_26_351783 98 18 and and CC 10_1101-2020_10_26_351783 98 19 obtaining obtain VBG 10_1101-2020_10_26_351783 98 20 Z z NN 10_1101-2020_10_26_351783 98 21 - - HYPH 10_1101-2020_10_26_351783 98 22 scores score NNS 10_1101-2020_10_26_351783 98 23 from from IN 10_1101-2020_10_26_351783 98 24 their -PRON- PRP$ 10_1101-2020_10_26_351783 98 25 distribution distribution NN 10_1101-2020_10_26_351783 98 26 . . . 10_1101-2020_10_26_351783 99 1 These these DT 10_1101-2020_10_26_351783 99 2 obtained obtain VBN 10_1101-2020_10_26_351783 99 3 gene gene NN 10_1101-2020_10_26_351783 99 4 scores score NNS 10_1101-2020_10_26_351783 99 5 are be VBP 10_1101-2020_10_26_351783 99 6 fused fuse VBN 10_1101-2020_10_26_351783 99 7 with with IN 10_1101-2020_10_26_351783 99 8 the the DT 10_1101-2020_10_26_351783 99 9 pathway pathway JJ 10_1101-2020_10_26_351783 99 10 enrichment enrichment NN 10_1101-2020_10_26_351783 99 11 analysis analysis NN 10_1101-2020_10_26_351783 99 12 to to TO 10_1101-2020_10_26_351783 99 13 recompute recompute VB 10_1101-2020_10_26_351783 99 14 a a DT 10_1101-2020_10_26_351783 99 15 chi chi JJ 10_1101-2020_10_26_351783 99 16 - - HYPH 10_1101-2020_10_26_351783 99 17 square square JJ 10_1101-2020_10_26_351783 99 18 P p NN 10_1101-2020_10_26_351783 99 19 - - HYPH 10_1101-2020_10_26_351783 99 20 value value NN 10_1101-2020_10_26_351783 99 21 for for IN 10_1101-2020_10_26_351783 99 22 the the DT 10_1101-2020_10_26_351783 99 23 given give VBN 10_1101-2020_10_26_351783 99 24 set set NN 10_1101-2020_10_26_351783 99 25 of of IN 10_1101-2020_10_26_351783 99 26 module module JJ 10_1101-2020_10_26_351783 99 27 genes gene NNS 10_1101-2020_10_26_351783 99 28 . . . 10_1101-2020_10_26_351783 100 1 Thus thus RB 10_1101-2020_10_26_351783 100 2 , , , 10_1101-2020_10_26_351783 100 3 the the DT 10_1101-2020_10_26_351783 100 4 obtained obtain VBN 10_1101-2020_10_26_351783 100 5 chi chi NNP 10_1101-2020_10_26_351783 100 6 - - HYPH 10_1101-2020_10_26_351783 100 7 square square JJ 10_1101-2020_10_26_351783 100 8 P- P- NNP 10_1101-2020_10_26_351783 100 9 value value NN 10_1101-2020_10_26_351783 100 10 serves serve VBZ 10_1101-2020_10_26_351783 100 11 as as IN 10_1101-2020_10_26_351783 100 12 the the DT 10_1101-2020_10_26_351783 100 13 significance significance NN 10_1101-2020_10_26_351783 100 14 of of IN 10_1101-2020_10_26_351783 100 15 the the DT 10_1101-2020_10_26_351783 100 16 module module NN 10_1101-2020_10_26_351783 100 17 in in IN 10_1101-2020_10_26_351783 100 18 its -PRON- PRP$ 10_1101-2020_10_26_351783 100 19 enrichment enrichment NN 10_1101-2020_10_26_351783 100 20 of of IN 10_1101-2020_10_26_351783 100 21 the the DT 10_1101-2020_10_26_351783 100 22 disease disease NN 10_1101-2020_10_26_351783 100 23 - - HYPH 10_1101-2020_10_26_351783 100 24 associated associate VBN 10_1101-2020_10_26_351783 100 25 pathway pathway JJ 10_1101-2020_10_26_351783 100 26 gene gene NN 10_1101-2020_10_26_351783 100 27 loci loci NNP 10_1101-2020_10_26_351783 100 28 . . . 10_1101-2020_10_26_351783 101 1 A a DT 10_1101-2020_10_26_351783 101 2 combined combined JJ 10_1101-2020_10_26_351783 101 3 P p NN 10_1101-2020_10_26_351783 101 4 - - HYPH 10_1101-2020_10_26_351783 101 5 value value NN 10_1101-2020_10_26_351783 101 6 was be VBD 10_1101-2020_10_26_351783 101 7 computed compute VBN 10_1101-2020_10_26_351783 101 8 for for IN 10_1101-2020_10_26_351783 101 9 each each DT 10_1101-2020_10_26_351783 101 10 of of IN 10_1101-2020_10_26_351783 101 11 the the DT 10_1101-2020_10_26_351783 101 12 methods method NNS 10_1101-2020_10_26_351783 101 13 using use VBG 10_1101-2020_10_26_351783 101 14 Fisher Fisher NNP 10_1101-2020_10_26_351783 101 15 ’s ’s POS 10_1101-2020_10_26_351783 101 16 method[19 method[19 NN 10_1101-2020_10_26_351783 101 17 ] ] -RRB- 10_1101-2020_10_26_351783 101 18 , , , 10_1101-2020_10_26_351783 101 19 diseases disease NNS 10_1101-2020_10_26_351783 101 20 , , , 10_1101-2020_10_26_351783 101 21 and and CC 10_1101-2020_10_26_351783 101 22 datasets dataset NNS 10_1101-2020_10_26_351783 101 23 for for IN 10_1101-2020_10_26_351783 101 24 ranking rank VBG 10_1101-2020_10_26_351783 101 25 the the DT 10_1101-2020_10_26_351783 101 26 performance performance NN 10_1101-2020_10_26_351783 101 27 of of IN 10_1101-2020_10_26_351783 101 28 the the DT 10_1101-2020_10_26_351783 101 29 modules module NNS 10_1101-2020_10_26_351783 101 30 in in IN 10_1101-2020_10_26_351783 101 31 each each DT 10_1101-2020_10_26_351783 101 32 criterion criterion NN 10_1101-2020_10_26_351783 101 33 . . . 10_1101-2020_10_26_351783 102 1 Integration integration NN 10_1101-2020_10_26_351783 102 2 of of IN 10_1101-2020_10_26_351783 102 3 MS MS NNP 10_1101-2020_10_26_351783 102 4 single single JJ 10_1101-2020_10_26_351783 102 5 - - HYPH 10_1101-2020_10_26_351783 102 6 omic omic JJ 10_1101-2020_10_26_351783 102 7 modules module NNS 10_1101-2020_10_26_351783 102 8 Clique Clique NNP 10_1101-2020_10_26_351783 102 9 SuM sum NN 10_1101-2020_10_26_351783 102 10 was be VBD 10_1101-2020_10_26_351783 102 11 ranked rank VBN 10_1101-2020_10_26_351783 102 12 as as IN 10_1101-2020_10_26_351783 102 13 the the DT 10_1101-2020_10_26_351783 102 14 best good JJS 10_1101-2020_10_26_351783 102 15 performing performing NN 10_1101-2020_10_26_351783 102 16 method method NN 10_1101-2020_10_26_351783 102 17 on on IN 10_1101-2020_10_26_351783 102 18 average average NN 10_1101-2020_10_26_351783 102 19 for for IN 10_1101-2020_10_26_351783 102 20 both both CC 10_1101-2020_10_26_351783 102 21 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 102 22 and and CC 10_1101-2020_10_26_351783 102 23 methylomic methylomic JJ 10_1101-2020_10_26_351783 102 24 data datum NNS 10_1101-2020_10_26_351783 102 25 , , , 10_1101-2020_10_26_351783 102 26 according accord VBG 10_1101-2020_10_26_351783 102 27 to to IN 10_1101-2020_10_26_351783 102 28 the the DT 10_1101-2020_10_26_351783 102 29 MS MS NNP 10_1101-2020_10_26_351783 102 30 GWAS GWAS NNP 10_1101-2020_10_26_351783 102 31 enrichment enrichment NN 10_1101-2020_10_26_351783 102 32 of of IN 10_1101-2020_10_26_351783 102 33 the the DT 10_1101-2020_10_26_351783 102 34 modules module NNS 10_1101-2020_10_26_351783 102 35 calculated calculate VBN 10_1101-2020_10_26_351783 102 36 by by IN 10_1101-2020_10_26_351783 102 37 Pascal Pascal NNP 10_1101-2020_10_26_351783 102 38 . . . 10_1101-2020_10_26_351783 103 1 Therefore therefore RB 10_1101-2020_10_26_351783 103 2 , , , 10_1101-2020_10_26_351783 103 3 significant significant JJ 10_1101-2020_10_26_351783 103 4 Clique Clique NNP 10_1101-2020_10_26_351783 103 5 SuM sum NN 10_1101-2020_10_26_351783 103 6 modules module NNS 10_1101-2020_10_26_351783 103 7 ( ( -LRB- 10_1101-2020_10_26_351783 103 8 P p NN 10_1101-2020_10_26_351783 103 9 < < XX 10_1101-2020_10_26_351783 103 10 0.05 0.05 XX 10_1101-2020_10_26_351783 103 11 ) ) -RRB- 10_1101-2020_10_26_351783 103 12 were be VBD 10_1101-2020_10_26_351783 103 13 selected select VBN 10_1101-2020_10_26_351783 103 14 for for IN 10_1101-2020_10_26_351783 103 15 further further JJ 10_1101-2020_10_26_351783 103 16 analysis analysis NN 10_1101-2020_10_26_351783 103 17 ( ( -LRB- 10_1101-2020_10_26_351783 103 18 nine nine CD 10_1101-2020_10_26_351783 103 19 transcriptomic transcriptomic NNP 10_1101-2020_10_26_351783 103 20 and and CC 10_1101-2020_10_26_351783 103 21 four four CD 10_1101-2020_10_26_351783 103 22 methylomic methylomic JJ 10_1101-2020_10_26_351783 103 23 modules module NNS 10_1101-2020_10_26_351783 103 24 ) ) -RRB- 10_1101-2020_10_26_351783 103 25 . . . 10_1101-2020_10_26_351783 104 1 Consensus consensus NN 10_1101-2020_10_26_351783 104 2 modules module NNS 10_1101-2020_10_26_351783 104 3 were be VBD 10_1101-2020_10_26_351783 104 4 generated generate VBN 10_1101-2020_10_26_351783 104 5 across across IN 10_1101-2020_10_26_351783 104 6 each each DT 10_1101-2020_10_26_351783 104 7 omic omic JJ 10_1101-2020_10_26_351783 104 8 by by IN 10_1101-2020_10_26_351783 104 9 applying apply VBG 10_1101-2020_10_26_351783 104 10 a a DT 10_1101-2020_10_26_351783 104 11 module module JJ 10_1101-2020_10_26_351783 104 12 count count NN 10_1101-2020_10_26_351783 104 13 - - HYPH 10_1101-2020_10_26_351783 104 14 based base VBN 10_1101-2020_10_26_351783 104 15 method method NN 10_1101-2020_10_26_351783 104 16 , , , 10_1101-2020_10_26_351783 104 17 where where WRB 10_1101-2020_10_26_351783 104 18 the the DT 10_1101-2020_10_26_351783 104 19 criteria criterion NNS 10_1101-2020_10_26_351783 104 20 for for IN 10_1101-2020_10_26_351783 104 21 gene gene NN 10_1101-2020_10_26_351783 104 22 inclusion inclusion NN 10_1101-2020_10_26_351783 104 23 in in IN 10_1101-2020_10_26_351783 104 24 the the DT 10_1101-2020_10_26_351783 104 25 consensus consensus NN 10_1101-2020_10_26_351783 104 26 is be VBZ 10_1101-2020_10_26_351783 104 27 its -PRON- PRP$ 10_1101-2020_10_26_351783 104 28 presence presence NN 10_1101-2020_10_26_351783 104 29 in in IN 10_1101-2020_10_26_351783 104 30 a a DT 10_1101-2020_10_26_351783 104 31 certain certain JJ 10_1101-2020_10_26_351783 104 32 number number NN 10_1101-2020_10_26_351783 104 33 of of IN 10_1101-2020_10_26_351783 104 34 single single JJ 10_1101-2020_10_26_351783 104 35 - - HYPH 10_1101-2020_10_26_351783 104 36 method method NN 10_1101-2020_10_26_351783 104 37 modules module NNS 10_1101-2020_10_26_351783 104 38 . . . 10_1101-2020_10_26_351783 105 1 To to TO 10_1101-2020_10_26_351783 105 2 balance balance VB 10_1101-2020_10_26_351783 105 3 the the DT 10_1101-2020_10_26_351783 105 4 weight weight NN 10_1101-2020_10_26_351783 105 5 of of IN 10_1101-2020_10_26_351783 105 6 each each DT 10_1101-2020_10_26_351783 105 7 omic omic JJ 10_1101-2020_10_26_351783 105 8 in in IN 10_1101-2020_10_26_351783 105 9 the the DT 10_1101-2020_10_26_351783 105 10 multi multi JJ 10_1101-2020_10_26_351783 105 11 - - NNS 10_1101-2020_10_26_351783 105 12 omics omic NNS 10_1101-2020_10_26_351783 105 13 integration integration NN 10_1101-2020_10_26_351783 105 14 , , , 10_1101-2020_10_26_351783 105 15 the the DT 10_1101-2020_10_26_351783 105 16 top top JJ 10_1101-2020_10_26_351783 105 17 four four CD 10_1101-2020_10_26_351783 105 18 significant significant JJ 10_1101-2020_10_26_351783 105 19 modules module NNS 10_1101-2020_10_26_351783 105 20 per per IN 10_1101-2020_10_26_351783 105 21 omic omic JJ 10_1101-2020_10_26_351783 105 22 were be VBD 10_1101-2020_10_26_351783 105 23 used use VBN 10_1101-2020_10_26_351783 105 24 to to TO 10_1101-2020_10_26_351783 105 25 create create VB 10_1101-2020_10_26_351783 105 26 each each DT 10_1101-2020_10_26_351783 105 27 consensus consensus NN 10_1101-2020_10_26_351783 105 28 ( ( -LRB- 10_1101-2020_10_26_351783 105 29 Fig fig NN 10_1101-2020_10_26_351783 105 30 . . . 10_1101-2020_10_26_351783 106 1 4a 4a NNP 10_1101-2020_10_26_351783 106 2 , , , 10_1101-2020_10_26_351783 106 3 b b NN 10_1101-2020_10_26_351783 106 4 ) ) -RRB- 10_1101-2020_10_26_351783 106 5 . . . 10_1101-2020_10_26_351783 107 1 Single single JJ 10_1101-2020_10_26_351783 107 2 - - HYPH 10_1101-2020_10_26_351783 107 3 omic omic JJ 10_1101-2020_10_26_351783 107 4 Clique Clique NNP 10_1101-2020_10_26_351783 107 5 SuM sum NN 10_1101-2020_10_26_351783 107 6 consensus consensus NN 10_1101-2020_10_26_351783 107 7 were be VBD 10_1101-2020_10_26_351783 107 8 ranked rank VBN 10_1101-2020_10_26_351783 107 9 again again RB 10_1101-2020_10_26_351783 107 10 by by IN 10_1101-2020_10_26_351783 107 11 GWAS GWAS NNP 10_1101-2020_10_26_351783 107 12 enrichment enrichment NN 10_1101-2020_10_26_351783 107 13 , , , 10_1101-2020_10_26_351783 107 14 and and CC 10_1101-2020_10_26_351783 107 15 the the DT 10_1101-2020_10_26_351783 107 16 best good JJS 10_1101-2020_10_26_351783 107 17 performing perform VBG 10_1101-2020_10_26_351783 107 18 consensus consensus NN 10_1101-2020_10_26_351783 107 19 per per IN 10_1101-2020_10_26_351783 107 20 omic omic JJ 10_1101-2020_10_26_351783 107 21 was be VBD 10_1101-2020_10_26_351783 107 22 selected select VBN 10_1101-2020_10_26_351783 107 23 for for IN 10_1101-2020_10_26_351783 107 24 integration integration NN 10_1101-2020_10_26_351783 107 25 into into IN 10_1101-2020_10_26_351783 107 26 the the DT 10_1101-2020_10_26_351783 107 27 multi multi JJ 10_1101-2020_10_26_351783 107 28 - - JJ 10_1101-2020_10_26_351783 107 29 omics omics JJ 10_1101-2020_10_26_351783 107 30 module module NN 10_1101-2020_10_26_351783 107 31 . . . 10_1101-2020_10_26_351783 108 1 Enrichment enrichment NN 10_1101-2020_10_26_351783 108 2 analyses analysis NNS 10_1101-2020_10_26_351783 108 3 of of IN 10_1101-2020_10_26_351783 108 4 the the DT 10_1101-2020_10_26_351783 108 5 MS MS NNP 10_1101-2020_10_26_351783 108 6 multi multi JJ 10_1101-2020_10_26_351783 108 7 - - HYPH 10_1101-2020_10_26_351783 108 8 omics omics JJ 10_1101-2020_10_26_351783 108 9 module module NNP 10_1101-2020_10_26_351783 108 10 Disease Disease NNP 10_1101-2020_10_26_351783 108 11 enrichment enrichment NN 10_1101-2020_10_26_351783 108 12 analysis analysis NN 10_1101-2020_10_26_351783 108 13 of of IN 10_1101-2020_10_26_351783 108 14 the the DT 10_1101-2020_10_26_351783 108 15 multi multi JJ 10_1101-2020_10_26_351783 108 16 - - NNS 10_1101-2020_10_26_351783 108 17 omics omic NNS 10_1101-2020_10_26_351783 108 18 module module NN 10_1101-2020_10_26_351783 108 19 was be VBD 10_1101-2020_10_26_351783 108 20 performed perform VBN 10_1101-2020_10_26_351783 108 21 by by IN 10_1101-2020_10_26_351783 108 22 Fisher Fisher NNP 10_1101-2020_10_26_351783 108 23 ’s ’s POS 10_1101-2020_10_26_351783 108 24 exact exact JJ 10_1101-2020_10_26_351783 108 25 test test NN 10_1101-2020_10_26_351783 108 26 , , , 10_1101-2020_10_26_351783 108 27 with with IN 10_1101-2020_10_26_351783 108 28 a a DT 10_1101-2020_10_26_351783 108 29 significance significance NN 10_1101-2020_10_26_351783 108 30 threshold threshold NN 10_1101-2020_10_26_351783 108 31 of of IN 10_1101-2020_10_26_351783 108 32 P p NN 10_1101-2020_10_26_351783 108 33 < < XX 10_1101-2020_10_26_351783 108 34 0.05 0.05 CD 10_1101-2020_10_26_351783 108 35 . . . 10_1101-2020_10_26_351783 109 1 MS MS NNP 10_1101-2020_10_26_351783 109 2 - - HYPH 10_1101-2020_10_26_351783 109 3 associated associate VBN 10_1101-2020_10_26_351783 109 4 genes gene NNS 10_1101-2020_10_26_351783 109 5 were be VBD 10_1101-2020_10_26_351783 109 6 obtained obtain VBN 10_1101-2020_10_26_351783 109 7 from from IN 10_1101-2020_10_26_351783 109 8 the the DT 10_1101-2020_10_26_351783 109 9 gene gene NN 10_1101-2020_10_26_351783 109 10 - - HYPH 10_1101-2020_10_26_351783 109 11 disease disease NNP 10_1101-2020_10_26_351783 109 12 association association NNP 10_1101-2020_10_26_351783 109 13 summary summary NN 10_1101-2020_10_26_351783 109 14 provided provide VBN 10_1101-2020_10_26_351783 109 15 by by IN 10_1101-2020_10_26_351783 109 16 DisGeNET DisGeNET NNP 10_1101-2020_10_26_351783 109 17 database database NN 10_1101-2020_10_26_351783 109 18 6.0[20] 6.0[20] NNP 10_1101-2020_10_26_351783 109 19 � � NNP 10_1101-2020_10_26_351783 109 20 . . . 10_1101-2020_10_26_351783 110 1 All all DT 10_1101-2020_10_26_351783 110 2 genes gene NNS 10_1101-2020_10_26_351783 110 3 with with IN 10_1101-2020_10_26_351783 110 4 a a DT 10_1101-2020_10_26_351783 110 5 known know VBN 10_1101-2020_10_26_351783 110 6 association association NN 10_1101-2020_10_26_351783 110 7 ( ( -LRB- 10_1101-2020_10_26_351783 110 8 which which WDT 10_1101-2020_10_26_351783 110 9 was be VBD 10_1101-2020_10_26_351783 110 10 not not RB 10_1101-2020_10_26_351783 110 11 certified certify VBN 10_1101-2020_10_26_351783 110 12 by by IN 10_1101-2020_10_26_351783 110 13 peer peer NN 10_1101-2020_10_26_351783 110 14 review review NN 10_1101-2020_10_26_351783 110 15 ) ) -RRB- 10_1101-2020_10_26_351783 110 16 is be VBZ 10_1101-2020_10_26_351783 110 17 the the DT 10_1101-2020_10_26_351783 110 18 author author NN 10_1101-2020_10_26_351783 110 19 / / SYM 10_1101-2020_10_26_351783 110 20 funder funder NN 10_1101-2020_10_26_351783 110 21 . . . 10_1101-2020_10_26_351783 111 1 All all DT 10_1101-2020_10_26_351783 111 2 rights right NNS 10_1101-2020_10_26_351783 111 3 reserved reserve VBD 10_1101-2020_10_26_351783 111 4 . . . 10_1101-2020_10_26_351783 112 1 No no DT 10_1101-2020_10_26_351783 112 2 reuse reuse NN 10_1101-2020_10_26_351783 112 3 allowed allow VBN 10_1101-2020_10_26_351783 112 4 without without IN 10_1101-2020_10_26_351783 112 5 permission permission NN 10_1101-2020_10_26_351783 112 6 . . . 10_1101-2020_10_26_351783 113 1 The the DT 10_1101-2020_10_26_351783 113 2 copyright copyright NN 10_1101-2020_10_26_351783 113 3 holder holder NN 10_1101-2020_10_26_351783 113 4 for for IN 10_1101-2020_10_26_351783 113 5 this this DT 10_1101-2020_10_26_351783 113 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 113 7 version version NN 10_1101-2020_10_26_351783 113 8 posted post VBD 10_1101-2020_10_26_351783 113 9 January January NNP 10_1101-2020_10_26_351783 113 10 6 6 CD 10_1101-2020_10_26_351783 113 11 , , , 10_1101-2020_10_26_351783 113 12 2021 2021 CD 10_1101-2020_10_26_351783 113 13 . . . 10_1101-2020_10_26_351783 113 14 ; ; : 10_1101-2020_10_26_351783 113 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 113 16 : : : 10_1101-2020_10_26_351783 113 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 113 18 preprint preprint NN 10_1101-2020_10_26_351783 113 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 113 20 9 9 CD 10_1101-2020_10_26_351783 113 21 to to IN 10_1101-2020_10_26_351783 113 22 the the DT 10_1101-2020_10_26_351783 113 23 disease disease NN 10_1101-2020_10_26_351783 113 24 “ " `` 10_1101-2020_10_26_351783 113 25 multiple multiple JJ 10_1101-2020_10_26_351783 113 26 sclerosis sclerosis NN 10_1101-2020_10_26_351783 113 27 ” " '' 10_1101-2020_10_26_351783 113 28 ( ( -LRB- 10_1101-2020_10_26_351783 113 29 Unified Unified NNP 10_1101-2020_10_26_351783 113 30 Medical Medical NNP 10_1101-2020_10_26_351783 113 31 Language Language NNP 10_1101-2020_10_26_351783 113 32 System System NNP 10_1101-2020_10_26_351783 113 33 unique unique JJ 10_1101-2020_10_26_351783 113 34 identifier identifi JJR 10_1101-2020_10_26_351783 113 35 C0026769 C0026769 NNP 10_1101-2020_10_26_351783 113 36 ) ) -RRB- 10_1101-2020_10_26_351783 113 37 were be VBD 10_1101-2020_10_26_351783 113 38 considered consider VBN 10_1101-2020_10_26_351783 113 39 MS MS NNP 10_1101-2020_10_26_351783 113 40 - - HYPH 10_1101-2020_10_26_351783 113 41 associated associate VBN 10_1101-2020_10_26_351783 113 42 genes gene NNS 10_1101-2020_10_26_351783 113 43 ( ( -LRB- 10_1101-2020_10_26_351783 113 44 n n NNP 10_1101-2020_10_26_351783 113 45 = = SYM 10_1101-2020_10_26_351783 113 46 1,105 1,105 CD 10_1101-2020_10_26_351783 113 47 ) ) -RRB- 10_1101-2020_10_26_351783 113 48 . . . 10_1101-2020_10_26_351783 114 1 Pathway pathway JJ 10_1101-2020_10_26_351783 114 2 enrichment enrichment NN 10_1101-2020_10_26_351783 114 3 analysis analysis NN 10_1101-2020_10_26_351783 114 4 was be VBD 10_1101-2020_10_26_351783 114 5 carried carry VBN 10_1101-2020_10_26_351783 114 6 out out RP 10_1101-2020_10_26_351783 114 7 using use VBG 10_1101-2020_10_26_351783 114 8 the the DT 10_1101-2020_10_26_351783 114 9 function function NN 10_1101-2020_10_26_351783 114 10 enrichKEGG enrichKEGG NNP 10_1101-2020_10_26_351783 114 11 from from IN 10_1101-2020_10_26_351783 114 12 the the DT 10_1101-2020_10_26_351783 114 13 clusterProfiler clusterprofiler NN 10_1101-2020_10_26_351783 114 14 R R NNP 10_1101-2020_10_26_351783 114 15 package[21 package[21 NNP 10_1101-2020_10_26_351783 114 16 ] ] -RRB- 10_1101-2020_10_26_351783 114 17 � � NNP 10_1101-2020_10_26_351783 114 18 , , , 10_1101-2020_10_26_351783 114 19 version version NN 10_1101-2020_10_26_351783 114 20 3.14.3 3.14.3 CD 10_1101-2020_10_26_351783 114 21 . . . 10_1101-2020_10_26_351783 115 1 P p NN 10_1101-2020_10_26_351783 115 2 - - HYPH 10_1101-2020_10_26_351783 115 3 values value NNS 10_1101-2020_10_26_351783 115 4 were be VBD 10_1101-2020_10_26_351783 115 5 adjusted adjust VBN 10_1101-2020_10_26_351783 115 6 for for IN 10_1101-2020_10_26_351783 115 7 multiple multiple JJ 10_1101-2020_10_26_351783 115 8 testing testing NN 10_1101-2020_10_26_351783 115 9 using use VBG 10_1101-2020_10_26_351783 115 10 Benjamini Benjamini NNP 10_1101-2020_10_26_351783 115 11 - - HYPH 10_1101-2020_10_26_351783 115 12 Hochberg Hochberg NNP 10_1101-2020_10_26_351783 115 13 FDR FDR NNP 10_1101-2020_10_26_351783 115 14 correction correction NN 10_1101-2020_10_26_351783 115 15 , , , 10_1101-2020_10_26_351783 115 16 with with IN 10_1101-2020_10_26_351783 115 17 a a DT 10_1101-2020_10_26_351783 115 18 significance significance NN 10_1101-2020_10_26_351783 115 19 threshold threshold NN 10_1101-2020_10_26_351783 115 20 of of IN 10_1101-2020_10_26_351783 115 21 adj adj NN 10_1101-2020_10_26_351783 115 22 . . . 10_1101-2020_10_26_351783 116 1 P p NN 10_1101-2020_10_26_351783 116 2 < < XX 10_1101-2020_10_26_351783 116 3 0.05 0.05 XX 10_1101-2020_10_26_351783 116 4 . . . 10_1101-2020_10_26_351783 117 1 Enrichment enrichment NN 10_1101-2020_10_26_351783 117 2 of of IN 10_1101-2020_10_26_351783 117 3 the the DT 10_1101-2020_10_26_351783 117 4 multi multi JJ 10_1101-2020_10_26_351783 117 5 - - JJ 10_1101-2020_10_26_351783 117 6 omics omics JJ 10_1101-2020_10_26_351783 117 7 module module NN 10_1101-2020_10_26_351783 117 8 in in IN 10_1101-2020_10_26_351783 117 9 MS MS NNP 10_1101-2020_10_26_351783 117 10 risk risk NN 10_1101-2020_10_26_351783 117 11 - - HYPH 10_1101-2020_10_26_351783 117 12 factor factor NN 10_1101-2020_10_26_351783 117 13 - - HYPH 10_1101-2020_10_26_351783 117 14 associated associate VBN 10_1101-2020_10_26_351783 117 15 genes gene NNS 10_1101-2020_10_26_351783 117 16 was be VBD 10_1101-2020_10_26_351783 117 17 performed perform VBN 10_1101-2020_10_26_351783 117 18 by by IN 10_1101-2020_10_26_351783 117 19 Fisher Fisher NNP 10_1101-2020_10_26_351783 117 20 ’s ’s POS 10_1101-2020_10_26_351783 117 21 exact exact JJ 10_1101-2020_10_26_351783 117 22 test test NN 10_1101-2020_10_26_351783 117 23 , , , 10_1101-2020_10_26_351783 117 24 with with IN 10_1101-2020_10_26_351783 117 25 a a DT 10_1101-2020_10_26_351783 117 26 significance significance NN 10_1101-2020_10_26_351783 117 27 threshold threshold NN 10_1101-2020_10_26_351783 117 28 of of IN 10_1101-2020_10_26_351783 117 29 P p NN 10_1101-2020_10_26_351783 117 30 < < XX 10_1101-2020_10_26_351783 117 31 0.05 0.05 CD 10_1101-2020_10_26_351783 117 32 . . . 10_1101-2020_10_26_351783 118 1 To to TO 10_1101-2020_10_26_351783 118 2 provide provide VB 10_1101-2020_10_26_351783 118 3 a a DT 10_1101-2020_10_26_351783 118 4 uniform uniform JJ 10_1101-2020_10_26_351783 118 5 comparison comparison NN 10_1101-2020_10_26_351783 118 6 of of IN 10_1101-2020_10_26_351783 118 7 MS MS NNP 10_1101-2020_10_26_351783 118 8 risk risk NN 10_1101-2020_10_26_351783 118 9 factor factor NN 10_1101-2020_10_26_351783 118 10 - - HYPH 10_1101-2020_10_26_351783 118 11 associated associate VBN 10_1101-2020_10_26_351783 118 12 genes gene NNS 10_1101-2020_10_26_351783 118 13 across across IN 10_1101-2020_10_26_351783 118 14 datasets dataset NNS 10_1101-2020_10_26_351783 118 15 , , , 10_1101-2020_10_26_351783 118 16 the the DT 10_1101-2020_10_26_351783 118 17 module module NN 10_1101-2020_10_26_351783 118 18 was be VBD 10_1101-2020_10_26_351783 118 19 tested test VBN 10_1101-2020_10_26_351783 118 20 for for IN 10_1101-2020_10_26_351783 118 21 enrichment enrichment NN 10_1101-2020_10_26_351783 118 22 in in IN 10_1101-2020_10_26_351783 118 23 the the DT 10_1101-2020_10_26_351783 118 24 top top JJ 10_1101-2020_10_26_351783 118 25 1,000 1,000 CD 10_1101-2020_10_26_351783 118 26 DMGs dmg NNS 10_1101-2020_10_26_351783 118 27 ( ( -LRB- 10_1101-2020_10_26_351783 118 28 with with IN 10_1101-2020_10_26_351783 118 29 at at RB 10_1101-2020_10_26_351783 118 30 least least JJS 10_1101-2020_10_26_351783 118 31 P p NN 10_1101-2020_10_26_351783 118 32 < < XX 10_1101-2020_10_26_351783 118 33 0.05 0.05 XX 10_1101-2020_10_26_351783 118 34 ) ) -RRB- 10_1101-2020_10_26_351783 118 35 obtained obtain VBN 10_1101-2020_10_26_351783 118 36 from from IN 10_1101-2020_10_26_351783 118 37 the the DT 10_1101-2020_10_26_351783 118 38 differential differential NN 10_1101-2020_10_26_351783 118 39 methylation methylation NN 10_1101-2020_10_26_351783 118 40 analysis analysis NN 10_1101-2020_10_26_351783 118 41 with with IN 10_1101-2020_10_26_351783 118 42 ChAMP ChAMP NNP 10_1101-2020_10_26_351783 118 43 for for IN 10_1101-2020_10_26_351783 118 44 each each DT 10_1101-2020_10_26_351783 118 45 risk risk NN 10_1101-2020_10_26_351783 118 46 factor factor NN 10_1101-2020_10_26_351783 118 47 dataset dataset NN 10_1101-2020_10_26_351783 118 48 . . . 10_1101-2020_10_26_351783 119 1 Representation representation NN 10_1101-2020_10_26_351783 119 2 of of IN 10_1101-2020_10_26_351783 119 3 the the DT 10_1101-2020_10_26_351783 119 4 MS MS NNP 10_1101-2020_10_26_351783 119 5 multi multi JJ 10_1101-2020_10_26_351783 119 6 - - HYPH 10_1101-2020_10_26_351783 119 7 omics omic NNS 10_1101-2020_10_26_351783 119 8 module module NN 10_1101-2020_10_26_351783 119 9 Experimentally experimentally RB 10_1101-2020_10_26_351783 119 10 validated validate VBD 10_1101-2020_10_26_351783 119 11 interactions interaction NNS 10_1101-2020_10_26_351783 119 12 for for IN 10_1101-2020_10_26_351783 119 13 the the DT 10_1101-2020_10_26_351783 119 14 multi multi JJ 10_1101-2020_10_26_351783 119 15 - - JJ 10_1101-2020_10_26_351783 119 16 omics omics JJ 10_1101-2020_10_26_351783 119 17 module module JJ 10_1101-2020_10_26_351783 119 18 genes gene NNS 10_1101-2020_10_26_351783 119 19 were be VBD 10_1101-2020_10_26_351783 119 20 obtained obtain VBN 10_1101-2020_10_26_351783 119 21 from from IN 10_1101-2020_10_26_351783 119 22 STRING string NN 10_1101-2020_10_26_351783 119 23 database database NN 10_1101-2020_10_26_351783 119 24 version version NN 10_1101-2020_10_26_351783 119 25 11 11 CD 10_1101-2020_10_26_351783 119 26 ( ( -LRB- 10_1101-2020_10_26_351783 119 27 experimental experimental JJ 10_1101-2020_10_26_351783 119 28 score score NN 10_1101-2020_10_26_351783 119 29 > > XX 10_1101-2020_10_26_351783 119 30 700 700 CD 10_1101-2020_10_26_351783 119 31 ) ) -RRB- 10_1101-2020_10_26_351783 119 32 and and CC 10_1101-2020_10_26_351783 119 33 imported import VBN 10_1101-2020_10_26_351783 119 34 into into IN 10_1101-2020_10_26_351783 119 35 Cytoscape[22 Cytoscape[22 NNP 10_1101-2020_10_26_351783 119 36 ] ] -RRB- 10_1101-2020_10_26_351783 119 37 version version NN 10_1101-2020_10_26_351783 119 38 3.7.2 3.7.2 CD 10_1101-2020_10_26_351783 119 39 . . . 10_1101-2020_10_26_351783 120 1 To to TO 10_1101-2020_10_26_351783 120 2 determine determine VB 10_1101-2020_10_26_351783 120 3 representative representative JJ 10_1101-2020_10_26_351783 120 4 functional functional JJ 10_1101-2020_10_26_351783 120 5 clusters cluster NNS 10_1101-2020_10_26_351783 120 6 of of IN 10_1101-2020_10_26_351783 120 7 module module JJ 10_1101-2020_10_26_351783 120 8 genes gene NNS 10_1101-2020_10_26_351783 120 9 , , , 10_1101-2020_10_26_351783 120 10 overrepresented overrepresente VBD 10_1101-2020_10_26_351783 120 11 Gene Gene NNP 10_1101-2020_10_26_351783 120 12 Ontology Ontology NNP 10_1101-2020_10_26_351783 120 13 ( ( -LRB- 10_1101-2020_10_26_351783 120 14 GO GO NNP 10_1101-2020_10_26_351783 120 15 ) ) -RRB- 10_1101-2020_10_26_351783 120 16 Biological Biological NNP 10_1101-2020_10_26_351783 120 17 Process Process NNP 10_1101-2020_10_26_351783 120 18 ( ( -LRB- 10_1101-2020_10_26_351783 120 19 BP BP NNP 10_1101-2020_10_26_351783 120 20 ) ) -RRB- 10_1101-2020_10_26_351783 120 21 terms term NNS 10_1101-2020_10_26_351783 120 22 in in IN 10_1101-2020_10_26_351783 120 23 the the DT 10_1101-2020_10_26_351783 120 24 module module NN 10_1101-2020_10_26_351783 120 25 were be VBD 10_1101-2020_10_26_351783 120 26 found find VBN 10_1101-2020_10_26_351783 120 27 using use VBG 10_1101-2020_10_26_351783 120 28 BiNGO[23 BiNGO[23 NNP 10_1101-2020_10_26_351783 120 29 ] ] -RRB- 10_1101-2020_10_26_351783 120 30 version version NN 10_1101-2020_10_26_351783 120 31 3.0.4 3.0.4 CD 10_1101-2020_10_26_351783 120 32 , , , 10_1101-2020_10_26_351783 120 33 with with IN 10_1101-2020_10_26_351783 120 34 Benjamini Benjamini NNP 10_1101-2020_10_26_351783 120 35 - - HYPH 10_1101-2020_10_26_351783 120 36 Hochberg Hochberg NNP 10_1101-2020_10_26_351783 120 37 FDR FDR NNP 10_1101-2020_10_26_351783 120 38 for for IN 10_1101-2020_10_26_351783 120 39 multiple multiple JJ 10_1101-2020_10_26_351783 120 40 testing testing NN 10_1101-2020_10_26_351783 120 41 correction correction NN 10_1101-2020_10_26_351783 120 42 , , , 10_1101-2020_10_26_351783 120 43 and and CC 10_1101-2020_10_26_351783 120 44 a a DT 10_1101-2020_10_26_351783 120 45 significance significance NN 10_1101-2020_10_26_351783 120 46 threshold threshold NN 10_1101-2020_10_26_351783 120 47 of of IN 10_1101-2020_10_26_351783 120 48 adj adj NN 10_1101-2020_10_26_351783 120 49 . . . 10_1101-2020_10_26_351783 121 1 P p NN 10_1101-2020_10_26_351783 121 2 < < XX 10_1101-2020_10_26_351783 121 3 0.05 0.05 XX 10_1101-2020_10_26_351783 121 4 . . . 10_1101-2020_10_26_351783 122 1 Then then RB 10_1101-2020_10_26_351783 122 2 , , , 10_1101-2020_10_26_351783 122 3 enriched enrich VBN 10_1101-2020_10_26_351783 122 4 GO GO NNP 10_1101-2020_10_26_351783 122 5 terms term NNS 10_1101-2020_10_26_351783 122 6 with with IN 10_1101-2020_10_26_351783 122 7 adj adj NN 10_1101-2020_10_26_351783 122 8 . . . 10_1101-2020_10_26_351783 123 1 P p NN 10_1101-2020_10_26_351783 123 2 < < XX 10_1101-2020_10_26_351783 123 3 1x10 1x10 CD 10_1101-2020_10_26_351783 123 4 - - SYM 10_1101-2020_10_26_351783 123 5 10 10 CD 10_1101-2020_10_26_351783 123 6 were be VBD 10_1101-2020_10_26_351783 123 7 summarized summarize VBN 10_1101-2020_10_26_351783 123 8 using use VBG 10_1101-2020_10_26_351783 123 9 REVIGO[24 revigo[24 ADD 10_1101-2020_10_26_351783 123 10 ] ] -RRB- 10_1101-2020_10_26_351783 123 11 server server NN 10_1101-2020_10_26_351783 123 12 tool tool NN 10_1101-2020_10_26_351783 123 13 ( ( -LRB- 10_1101-2020_10_26_351783 123 14 medium medium NNP 10_1101-2020_10_26_351783 123 15 allowed allow VBN 10_1101-2020_10_26_351783 123 16 similarity similarity NN 10_1101-2020_10_26_351783 123 17 = = SYM 10_1101-2020_10_26_351783 123 18 0.7 0.7 CD 10_1101-2020_10_26_351783 123 19 ) ) -RRB- 10_1101-2020_10_26_351783 123 20 and and CC 10_1101-2020_10_26_351783 123 21 categories category NNS 10_1101-2020_10_26_351783 123 22 of of IN 10_1101-2020_10_26_351783 123 23 interest interest NN 10_1101-2020_10_26_351783 123 24 were be VBD 10_1101-2020_10_26_351783 123 25 selected select VBN 10_1101-2020_10_26_351783 123 26 by by IN 10_1101-2020_10_26_351783 123 27 uniqueness uniqueness NN 10_1101-2020_10_26_351783 123 28 ( ( -LRB- 10_1101-2020_10_26_351783 123 29 > > XX 10_1101-2020_10_26_351783 123 30 = = SYM 10_1101-2020_10_26_351783 123 31 80 80 CD 10_1101-2020_10_26_351783 123 32 % % NN 10_1101-2020_10_26_351783 123 33 ) ) -RRB- 10_1101-2020_10_26_351783 123 34 , , , 10_1101-2020_10_26_351783 123 35 dispensability dispensability NN 10_1101-2020_10_26_351783 123 36 ( ( -LRB- 10_1101-2020_10_26_351783 123 37 > > XX 10_1101-2020_10_26_351783 123 38 = = SYM 10_1101-2020_10_26_351783 123 39 50 50 CD 10_1101-2020_10_26_351783 123 40 % % NN 10_1101-2020_10_26_351783 123 41 ) ) -RRB- 10_1101-2020_10_26_351783 123 42 , , , 10_1101-2020_10_26_351783 123 43 and and CC 10_1101-2020_10_26_351783 123 44 frequency frequency NN 10_1101-2020_10_26_351783 123 45 ( ( -LRB- 10_1101-2020_10_26_351783 123 46 < < XX 10_1101-2020_10_26_351783 123 47 = = SYM 10_1101-2020_10_26_351783 123 48 10 10 CD 10_1101-2020_10_26_351783 123 49 % % NN 10_1101-2020_10_26_351783 123 50 ) ) -RRB- 10_1101-2020_10_26_351783 123 51 criteria criterion NNS 10_1101-2020_10_26_351783 123 52 . . . 10_1101-2020_10_26_351783 124 1 Further further JJ 10_1101-2020_10_26_351783 124 2 manual manual JJ 10_1101-2020_10_26_351783 124 3 assessment assessment NN 10_1101-2020_10_26_351783 124 4 was be VBD 10_1101-2020_10_26_351783 124 5 performed perform VBN 10_1101-2020_10_26_351783 124 6 to to TO 10_1101-2020_10_26_351783 124 7 group group VB 10_1101-2020_10_26_351783 124 8 similar similar JJ 10_1101-2020_10_26_351783 124 9 terms term NNS 10_1101-2020_10_26_351783 124 10 with with IN 10_1101-2020_10_26_351783 124 11 an an DT 10_1101-2020_10_26_351783 124 12 adequate adequate JJ 10_1101-2020_10_26_351783 124 13 number number NN 10_1101-2020_10_26_351783 124 14 of of IN 10_1101-2020_10_26_351783 124 15 genes gene NNS 10_1101-2020_10_26_351783 124 16 in in IN 10_1101-2020_10_26_351783 124 17 the the DT 10_1101-2020_10_26_351783 124 18 network network NN 10_1101-2020_10_26_351783 124 19 . . . 10_1101-2020_10_26_351783 125 1 RESULTS RESULTS NNP 10_1101-2020_10_26_351783 125 2 A a DT 10_1101-2020_10_26_351783 125 3 benchmark benchmark NN 10_1101-2020_10_26_351783 125 4 comparing compare VBG 10_1101-2020_10_26_351783 125 5 337 337 CD 10_1101-2020_10_26_351783 125 6 transcriptionally transcriptionally RB 10_1101-2020_10_26_351783 125 7 derived derive VBN 10_1101-2020_10_26_351783 125 8 disease disease NN 10_1101-2020_10_26_351783 125 9 modules module NNS 10_1101-2020_10_26_351783 125 10 from from IN 10_1101-2020_10_26_351783 125 11 19 19 CD 10_1101-2020_10_26_351783 125 12 different different JJ 10_1101-2020_10_26_351783 125 13 diseases disease NNS 10_1101-2020_10_26_351783 125 14 . . . 10_1101-2020_10_26_351783 126 1 We -PRON- PRP 10_1101-2020_10_26_351783 126 2 compiled compile VBD 10_1101-2020_10_26_351783 126 3 a a DT 10_1101-2020_10_26_351783 126 4 benchmark benchmark JJ 10_1101-2020_10_26_351783 126 5 source source NN 10_1101-2020_10_26_351783 126 6 of of IN 10_1101-2020_10_26_351783 126 7 disease disease NNP 10_1101-2020_10_26_351783 126 8 modules module NNS 10_1101-2020_10_26_351783 126 9 and and CC 10_1101-2020_10_26_351783 126 10 summary summary NN 10_1101-2020_10_26_351783 126 11 statistics statistic NNS 10_1101-2020_10_26_351783 126 12 of of IN 10_1101-2020_10_26_351783 126 13 GWAS GWAS NNP 10_1101-2020_10_26_351783 126 14 datasets dataset NNS 10_1101-2020_10_26_351783 126 15 from from IN 10_1101-2020_10_26_351783 126 16 19 19 CD 10_1101-2020_10_26_351783 126 17 well well RB 10_1101-2020_10_26_351783 126 18 - - HYPH 10_1101-2020_10_26_351783 126 19 powered power VBN 10_1101-2020_10_26_351783 126 20 case case NN 10_1101-2020_10_26_351783 126 21 - - HYPH 10_1101-2020_10_26_351783 126 22 control control NN 10_1101-2020_10_26_351783 126 23 studies study NNS 10_1101-2020_10_26_351783 126 24 ( ( -LRB- 10_1101-2020_10_26_351783 126 25 Supplementary Supplementary NNP 10_1101-2020_10_26_351783 126 26 Table Table NNP 10_1101-2020_10_26_351783 126 27 1 1 CD 10_1101-2020_10_26_351783 126 28 ) ) -RRB- 10_1101-2020_10_26_351783 126 29 , , , 10_1101-2020_10_26_351783 126 30 some some DT 10_1101-2020_10_26_351783 126 31 of of IN 10_1101-2020_10_26_351783 126 32 which which WDT 10_1101-2020_10_26_351783 126 33 were be VBD 10_1101-2020_10_26_351783 126 34 previously previously RB 10_1101-2020_10_26_351783 126 35 used use VBN 10_1101-2020_10_26_351783 126 36 in in IN 10_1101-2020_10_26_351783 126 37 the the DT 10_1101-2020_10_26_351783 126 38 DREAM dream JJ 10_1101-2020_10_26_351783 126 39 topological topological JJ 10_1101-2020_10_26_351783 126 40 disease disease NN 10_1101-2020_10_26_351783 126 41 module module NNP 10_1101-2020_10_26_351783 126 42 challenge[12 challenge[12 NNP 10_1101-2020_10_26_351783 126 43 ] ] -RRB- 10_1101-2020_10_26_351783 126 44 . . . 10_1101-2020_10_26_351783 127 1 For for IN 10_1101-2020_10_26_351783 127 2 these these DT 10_1101-2020_10_26_351783 127 3 datasets dataset NNS 10_1101-2020_10_26_351783 127 4 we -PRON- PRP 10_1101-2020_10_26_351783 127 5 assessed assess VBD 10_1101-2020_10_26_351783 127 6 modules module NNS 10_1101-2020_10_26_351783 127 7 using use VBG 10_1101-2020_10_26_351783 127 8 the the DT 10_1101-2020_10_26_351783 127 9 same same JJ 10_1101-2020_10_26_351783 127 10 metric metric NN 10_1101-2020_10_26_351783 127 11 as as IN 10_1101-2020_10_26_351783 127 12 in in IN 10_1101-2020_10_26_351783 127 13 the the DT 10_1101-2020_10_26_351783 127 14 recent recent JJ 10_1101-2020_10_26_351783 127 15 DREAM DREAM NNP 10_1101-2020_10_26_351783 127 16 study[12 study[12 NN 10_1101-2020_10_26_351783 127 17 ] ] -RRB- 10_1101-2020_10_26_351783 127 18 , , , 10_1101-2020_10_26_351783 127 19 based base VBN 10_1101-2020_10_26_351783 127 20 on on IN 10_1101-2020_10_26_351783 127 21 the the DT 10_1101-2020_10_26_351783 127 22 pathway pathway NN 10_1101-2020_10_26_351783 127 23 scoring scoring NN 10_1101-2020_10_26_351783 127 24 ( ( -LRB- 10_1101-2020_10_26_351783 127 25 which which WDT 10_1101-2020_10_26_351783 127 26 was be VBD 10_1101-2020_10_26_351783 127 27 not not RB 10_1101-2020_10_26_351783 127 28 certified certify VBN 10_1101-2020_10_26_351783 127 29 by by IN 10_1101-2020_10_26_351783 127 30 peer peer NN 10_1101-2020_10_26_351783 127 31 review review NN 10_1101-2020_10_26_351783 127 32 ) ) -RRB- 10_1101-2020_10_26_351783 127 33 is be VBZ 10_1101-2020_10_26_351783 127 34 the the DT 10_1101-2020_10_26_351783 127 35 author author NN 10_1101-2020_10_26_351783 127 36 / / SYM 10_1101-2020_10_26_351783 127 37 funder funder NN 10_1101-2020_10_26_351783 127 38 . . . 10_1101-2020_10_26_351783 128 1 All all DT 10_1101-2020_10_26_351783 128 2 rights right NNS 10_1101-2020_10_26_351783 128 3 reserved reserve VBD 10_1101-2020_10_26_351783 128 4 . . . 10_1101-2020_10_26_351783 129 1 No no DT 10_1101-2020_10_26_351783 129 2 reuse reuse NN 10_1101-2020_10_26_351783 129 3 allowed allow VBN 10_1101-2020_10_26_351783 129 4 without without IN 10_1101-2020_10_26_351783 129 5 permission permission NN 10_1101-2020_10_26_351783 129 6 . . . 10_1101-2020_10_26_351783 130 1 The the DT 10_1101-2020_10_26_351783 130 2 copyright copyright NN 10_1101-2020_10_26_351783 130 3 holder holder NN 10_1101-2020_10_26_351783 130 4 for for IN 10_1101-2020_10_26_351783 130 5 this this DT 10_1101-2020_10_26_351783 130 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 130 7 version version NN 10_1101-2020_10_26_351783 130 8 posted post VBD 10_1101-2020_10_26_351783 130 9 January January NNP 10_1101-2020_10_26_351783 130 10 6 6 CD 10_1101-2020_10_26_351783 130 11 , , , 10_1101-2020_10_26_351783 130 12 2021 2021 CD 10_1101-2020_10_26_351783 130 13 . . . 10_1101-2020_10_26_351783 130 14 ; ; : 10_1101-2020_10_26_351783 130 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 130 16 : : : 10_1101-2020_10_26_351783 130 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 130 18 preprint preprint NN 10_1101-2020_10_26_351783 130 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 130 20 10 10 CD 10_1101-2020_10_26_351783 130 21 algorithm algorithm NN 10_1101-2020_10_26_351783 130 22 ( ( -LRB- 10_1101-2020_10_26_351783 130 23 Pascal)[18 pascal)[18 NN 10_1101-2020_10_26_351783 130 24 ] ] -RRB- 10_1101-2020_10_26_351783 130 25 . . . 10_1101-2020_10_26_351783 131 1 For for IN 10_1101-2020_10_26_351783 131 2 each each DT 10_1101-2020_10_26_351783 131 3 disease disease NN 10_1101-2020_10_26_351783 131 4 we -PRON- PRP 10_1101-2020_10_26_351783 131 5 compiled compile VBD 10_1101-2020_10_26_351783 131 6 one one CD 10_1101-2020_10_26_351783 131 7 to to TO 10_1101-2020_10_26_351783 131 8 five five CD 10_1101-2020_10_26_351783 131 9 publicly publicly RB 10_1101-2020_10_26_351783 131 10 available available JJ 10_1101-2020_10_26_351783 131 11 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 131 12 datasets dataset NNS 10_1101-2020_10_26_351783 131 13 considering consider VBG 10_1101-2020_10_26_351783 131 14 both both CC 10_1101-2020_10_26_351783 131 15 easily easily RB 10_1101-2020_10_26_351783 131 16 assessable assessable JJ 10_1101-2020_10_26_351783 131 17 tissues tissue NNS 10_1101-2020_10_26_351783 131 18 ( ( -LRB- 10_1101-2020_10_26_351783 131 19 e.g. e.g. RB 10_1101-2020_10_26_351783 132 1 blood blood NN 10_1101-2020_10_26_351783 132 2 ) ) -RRB- 10_1101-2020_10_26_351783 132 3 and and CC 10_1101-2020_10_26_351783 132 4 target target VB 10_1101-2020_10_26_351783 132 5 tissues tissue NNS 10_1101-2020_10_26_351783 132 6 , , , 10_1101-2020_10_26_351783 132 7 thereby thereby RB 10_1101-2020_10_26_351783 132 8 covering cover VBG 10_1101-2020_10_26_351783 132 9 47 47 CD 10_1101-2020_10_26_351783 132 10 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 132 11 datasets dataset NNS 10_1101-2020_10_26_351783 132 12 in in IN 10_1101-2020_10_26_351783 132 13 total total NN 10_1101-2020_10_26_351783 132 14 ( ( -LRB- 10_1101-2020_10_26_351783 132 15 Fig fig NN 10_1101-2020_10_26_351783 132 16 . . . 10_1101-2020_10_26_351783 133 1 1a 1a LS 10_1101-2020_10_26_351783 133 2 ) ) -RRB- 10_1101-2020_10_26_351783 133 3 . . . 10_1101-2020_10_26_351783 134 1 Modules module NNS 10_1101-2020_10_26_351783 134 2 were be VBD 10_1101-2020_10_26_351783 134 3 created create VBN 10_1101-2020_10_26_351783 134 4 using use VBG 10_1101-2020_10_26_351783 134 5 eight eight CD 10_1101-2020_10_26_351783 134 6 different different JJ 10_1101-2020_10_26_351783 134 7 methods method NNS 10_1101-2020_10_26_351783 134 8 from from IN 10_1101-2020_10_26_351783 134 9 MODifieR[13 MODifieR[13 NNP 10_1101-2020_10_26_351783 134 10 ] ] -RRB- 10_1101-2020_10_26_351783 134 11 . . . 10_1101-2020_10_26_351783 135 1 In in IN 10_1101-2020_10_26_351783 135 2 addition addition NN 10_1101-2020_10_26_351783 135 3 , , , 10_1101-2020_10_26_351783 135 4 we -PRON- PRP 10_1101-2020_10_26_351783 135 5 also also RB 10_1101-2020_10_26_351783 135 6 tested test VBD 10_1101-2020_10_26_351783 135 7 if if IN 10_1101-2020_10_26_351783 135 8 genes gene NNS 10_1101-2020_10_26_351783 135 9 detected detect VBN 10_1101-2020_10_26_351783 135 10 by by IN 10_1101-2020_10_26_351783 135 11 several several JJ 10_1101-2020_10_26_351783 135 12 methods method NNS 10_1101-2020_10_26_351783 135 13 , , , 10_1101-2020_10_26_351783 135 14 hereafter hereafter RB 10_1101-2020_10_26_351783 135 15 called call VBN 10_1101-2020_10_26_351783 135 16 consensus consensus NN 10_1101-2020_10_26_351783 135 17 module module NNP 10_1101-2020_10_26_351783 135 18 genes gene NNS 10_1101-2020_10_26_351783 135 19 , , , 10_1101-2020_10_26_351783 135 20 had have VBD 10_1101-2020_10_26_351783 135 21 higher high JJR 10_1101-2020_10_26_351783 135 22 enrichment enrichment NN 10_1101-2020_10_26_351783 135 23 scores score NNS 10_1101-2020_10_26_351783 135 24 than than IN 10_1101-2020_10_26_351783 135 25 single single JJ 10_1101-2020_10_26_351783 135 26 - - HYPH 10_1101-2020_10_26_351783 135 27 method method NN 10_1101-2020_10_26_351783 135 28 module module JJ 10_1101-2020_10_26_351783 135 29 genes gene NNS 10_1101-2020_10_26_351783 135 30 . . . 10_1101-2020_10_26_351783 136 1 Enrichment enrichment NN 10_1101-2020_10_26_351783 136 2 scores score NNS 10_1101-2020_10_26_351783 136 3 for for IN 10_1101-2020_10_26_351783 136 4 the the DT 10_1101-2020_10_26_351783 136 5 non non JJ 10_1101-2020_10_26_351783 136 6 - - JJ 10_1101-2020_10_26_351783 136 7 empty empty JJ 10_1101-2020_10_26_351783 136 8 modules module NNS 10_1101-2020_10_26_351783 136 9 ( ( -LRB- 10_1101-2020_10_26_351783 136 10 n n NNP 10_1101-2020_10_26_351783 136 11 = = SYM 10_1101-2020_10_26_351783 136 12 337 337 CD 10_1101-2020_10_26_351783 136 13 ) ) -RRB- 10_1101-2020_10_26_351783 136 14 from from IN 10_1101-2020_10_26_351783 136 15 this this DT 10_1101-2020_10_26_351783 136 16 analysis analysis NN 10_1101-2020_10_26_351783 136 17 were be VBD 10_1101-2020_10_26_351783 136 18 summarized summarize VBN 10_1101-2020_10_26_351783 136 19 for for IN 10_1101-2020_10_26_351783 136 20 each each DT 10_1101-2020_10_26_351783 136 21 method method NN 10_1101-2020_10_26_351783 136 22 and and CC 10_1101-2020_10_26_351783 136 23 dataset dataset NN 10_1101-2020_10_26_351783 136 24 ( ( -LRB- 10_1101-2020_10_26_351783 136 25 Fig fig NN 10_1101-2020_10_26_351783 136 26 . . . 10_1101-2020_10_26_351783 137 1 2a 2a LS 10_1101-2020_10_26_351783 137 2 ) ) -RRB- 10_1101-2020_10_26_351783 137 3 . . . 10_1101-2020_10_26_351783 138 1 In in IN 10_1101-2020_10_26_351783 138 2 total total NN 10_1101-2020_10_26_351783 138 3 , , , 10_1101-2020_10_26_351783 138 4 we -PRON- PRP 10_1101-2020_10_26_351783 138 5 found find VBD 10_1101-2020_10_26_351783 138 6 significantly significantly RB 10_1101-2020_10_26_351783 138 7 GWAS gwa VBN 10_1101-2020_10_26_351783 138 8 - - HYPH 10_1101-2020_10_26_351783 138 9 enriched enrich VBN 10_1101-2020_10_26_351783 138 10 modules module NNS 10_1101-2020_10_26_351783 138 11 in in IN 10_1101-2020_10_26_351783 138 12 17.8 17.8 CD 10_1101-2020_10_26_351783 138 13 % % NN 10_1101-2020_10_26_351783 138 14 ( ( -LRB- 10_1101-2020_10_26_351783 138 15 60/337 60/337 CD 10_1101-2020_10_26_351783 138 16 ) ) -RRB- 10_1101-2020_10_26_351783 138 17 of of IN 10_1101-2020_10_26_351783 138 18 the the DT 10_1101-2020_10_26_351783 138 19 single single JJ 10_1101-2020_10_26_351783 138 20 - - HYPH 10_1101-2020_10_26_351783 138 21 method method NN 10_1101-2020_10_26_351783 138 22 modules module NNS 10_1101-2020_10_26_351783 138 23 and and CC 10_1101-2020_10_26_351783 138 24 25.5 25.5 CD 10_1101-2020_10_26_351783 138 25 % % NN 10_1101-2020_10_26_351783 138 26 ( ( -LRB- 10_1101-2020_10_26_351783 138 27 12/47 12/47 CD 10_1101-2020_10_26_351783 138 28 ) ) -RRB- 10_1101-2020_10_26_351783 138 29 of of IN 10_1101-2020_10_26_351783 138 30 the the DT 10_1101-2020_10_26_351783 138 31 non non JJ 10_1101-2020_10_26_351783 138 32 - - JJ 10_1101-2020_10_26_351783 138 33 empty empty JJ 10_1101-2020_10_26_351783 138 34 consensus consensus NN 10_1101-2020_10_26_351783 138 35 modules module NNS 10_1101-2020_10_26_351783 138 36 that that IN 10_1101-2020_10_26_351783 138 37 combined combine VBD 10_1101-2020_10_26_351783 138 38 at at RB 10_1101-2020_10_26_351783 138 39 least least RBS 10_1101-2020_10_26_351783 138 40 three three CD 10_1101-2020_10_26_351783 138 41 methods method NNS 10_1101-2020_10_26_351783 138 42 as as IN 10_1101-2020_10_26_351783 138 43 a a DT 10_1101-2020_10_26_351783 138 44 criterion criterion NN 10_1101-2020_10_26_351783 138 45 . . . 10_1101-2020_10_26_351783 139 1 These these DT 10_1101-2020_10_26_351783 139 2 numbers number NNS 10_1101-2020_10_26_351783 139 3 seemed seem VBD 10_1101-2020_10_26_351783 139 4 higher high JJR 10_1101-2020_10_26_351783 139 5 than than IN 10_1101-2020_10_26_351783 139 6 expected expect VBN 10_1101-2020_10_26_351783 139 7 , , , 10_1101-2020_10_26_351783 139 8 which which WDT 10_1101-2020_10_26_351783 139 9 might may MD 10_1101-2020_10_26_351783 139 10 have have VB 10_1101-2020_10_26_351783 139 11 been be VBN 10_1101-2020_10_26_351783 139 12 a a DT 10_1101-2020_10_26_351783 139 13 consequence consequence NN 10_1101-2020_10_26_351783 139 14 of of IN 10_1101-2020_10_26_351783 139 15 the the DT 10_1101-2020_10_26_351783 139 16 same same JJ 10_1101-2020_10_26_351783 139 17 GWAS GWAS NNP 10_1101-2020_10_26_351783 139 18 being be VBG 10_1101-2020_10_26_351783 139 19 used use VBN 10_1101-2020_10_26_351783 139 20 to to TO 10_1101-2020_10_26_351783 139 21 evaluate evaluate VB 10_1101-2020_10_26_351783 139 22 multiple multiple JJ 10_1101-2020_10_26_351783 139 23 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 139 24 datasets dataset NNS 10_1101-2020_10_26_351783 139 25 of of IN 10_1101-2020_10_26_351783 139 26 the the DT 10_1101-2020_10_26_351783 139 27 same same JJ 10_1101-2020_10_26_351783 139 28 disease disease NN 10_1101-2020_10_26_351783 139 29 . . . 10_1101-2020_10_26_351783 140 1 Hence hence RB 10_1101-2020_10_26_351783 140 2 , , , 10_1101-2020_10_26_351783 140 3 we -PRON- PRP 10_1101-2020_10_26_351783 140 4 aggregated aggregate VBD 10_1101-2020_10_26_351783 140 5 scores score NNS 10_1101-2020_10_26_351783 140 6 of of IN 10_1101-2020_10_26_351783 140 7 the the DT 10_1101-2020_10_26_351783 140 8 same same JJ 10_1101-2020_10_26_351783 140 9 disease disease NN 10_1101-2020_10_26_351783 140 10 and and CC 10_1101-2020_10_26_351783 140 11 method method NN 10_1101-2020_10_26_351783 140 12 as as IN 10_1101-2020_10_26_351783 140 13 meta meta JJ 10_1101-2020_10_26_351783 140 14 P p NN 10_1101-2020_10_26_351783 140 15 - - HYPH 10_1101-2020_10_26_351783 140 16 values value NNS 10_1101-2020_10_26_351783 140 17 ( ( -LRB- 10_1101-2020_10_26_351783 140 18 see see VB 10_1101-2020_10_26_351783 140 19 Methods method NNS 10_1101-2020_10_26_351783 140 20 ) ) -RRB- 10_1101-2020_10_26_351783 140 21 . . . 10_1101-2020_10_26_351783 141 1 Out out IN 10_1101-2020_10_26_351783 141 2 of of IN 10_1101-2020_10_26_351783 141 3 the the DT 10_1101-2020_10_26_351783 141 4 152 152 CD 10_1101-2020_10_26_351783 141 5 possible possible JJ 10_1101-2020_10_26_351783 141 6 disease disease NN 10_1101-2020_10_26_351783 141 7 - - HYPH 10_1101-2020_10_26_351783 141 8 method method NN 10_1101-2020_10_26_351783 141 9 combinations combination NNS 10_1101-2020_10_26_351783 141 10 , , , 10_1101-2020_10_26_351783 141 11 18 18 CD 10_1101-2020_10_26_351783 141 12 % % NN 10_1101-2020_10_26_351783 141 13 of of IN 10_1101-2020_10_26_351783 141 14 the the DT 10_1101-2020_10_26_351783 141 15 pairs pair NNS 10_1101-2020_10_26_351783 141 16 showed show VBD 10_1101-2020_10_26_351783 141 17 a a DT 10_1101-2020_10_26_351783 141 18 significant significant JJ 10_1101-2020_10_26_351783 141 19 GWAS GWAS NNP 10_1101-2020_10_26_351783 141 20 Pascal pascal JJ 10_1101-2020_10_26_351783 141 21 enrichment enrichment NN 10_1101-2020_10_26_351783 141 22 , , , 10_1101-2020_10_26_351783 141 23 which which WDT 10_1101-2020_10_26_351783 141 24 is be VBZ 10_1101-2020_10_26_351783 141 25 more more JJR 10_1101-2020_10_26_351783 141 26 than than IN 10_1101-2020_10_26_351783 141 27 expected expect VBN 10_1101-2020_10_26_351783 141 28 by by IN 10_1101-2020_10_26_351783 141 29 chance chance NN 10_1101-2020_10_26_351783 141 30 ( ( -LRB- 10_1101-2020_10_26_351783 141 31 n n NN 10_1101-2020_10_26_351783 141 32 = = SYM 10_1101-2020_10_26_351783 141 33 27 27 CD 10_1101-2020_10_26_351783 141 34 , , , 10_1101-2020_10_26_351783 141 35 P p NN 10_1101-2020_10_26_351783 141 36 = = SYM 10_1101-2020_10_26_351783 141 37 1.0 1.0 CD 10_1101-2020_10_26_351783 141 38 x x SYM 10_1101-2020_10_26_351783 141 39 10 10 CD 10_1101-2020_10_26_351783 141 40 - - SYM 10_1101-2020_10_26_351783 141 41 8 8 CD 10_1101-2020_10_26_351783 141 42 ) ) -RRB- 10_1101-2020_10_26_351783 141 43 . . . 10_1101-2020_10_26_351783 142 1 The the DT 10_1101-2020_10_26_351783 142 2 most most RBS 10_1101-2020_10_26_351783 142 3 enriched enriched JJ 10_1101-2020_10_26_351783 142 4 method method NN 10_1101-2020_10_26_351783 142 5 was be VBD 10_1101-2020_10_26_351783 142 6 Clique Clique NNP 10_1101-2020_10_26_351783 142 7 SuM sum NN 10_1101-2020_10_26_351783 142 8 , , , 10_1101-2020_10_26_351783 142 9 which which WDT 10_1101-2020_10_26_351783 142 10 showed show VBD 10_1101-2020_10_26_351783 142 11 significant significant JJ 10_1101-2020_10_26_351783 142 12 enrichment enrichment NN 10_1101-2020_10_26_351783 142 13 in in IN 10_1101-2020_10_26_351783 142 14 seven seven CD 10_1101-2020_10_26_351783 142 15 out out IN 10_1101-2020_10_26_351783 142 16 of of IN 10_1101-2020_10_26_351783 142 17 19 19 CD 10_1101-2020_10_26_351783 142 18 diseases disease NNS 10_1101-2020_10_26_351783 142 19 ( ( -LRB- 10_1101-2020_10_26_351783 142 20 binomial binomial JJ 10_1101-2020_10_26_351783 142 21 test test NN 10_1101-2020_10_26_351783 142 22 P p NN 10_1101-2020_10_26_351783 142 23 = = SYM 10_1101-2020_10_26_351783 142 24 2.3 2.3 CD 10_1101-2020_10_26_351783 142 25 x x SYM 10_1101-2020_10_26_351783 142 26 10 10 CD 10_1101-2020_10_26_351783 142 27 - - SYM 10_1101-2020_10_26_351783 142 28 5 5 CD 10_1101-2020_10_26_351783 142 29 ) ) -RRB- 10_1101-2020_10_26_351783 142 30 . . . 10_1101-2020_10_26_351783 143 1 Many many JJ 10_1101-2020_10_26_351783 143 2 methods method NNS 10_1101-2020_10_26_351783 143 3 exhibited exhibit VBD 10_1101-2020_10_26_351783 143 4 strong strong JJ 10_1101-2020_10_26_351783 143 5 enrichments enrichment NNS 10_1101-2020_10_26_351783 143 6 in in IN 10_1101-2020_10_26_351783 143 7 coronary coronary JJ 10_1101-2020_10_26_351783 143 8 artery artery NN 10_1101-2020_10_26_351783 143 9 disease disease NN 10_1101-2020_10_26_351783 143 10 ( ( -LRB- 10_1101-2020_10_26_351783 143 11 CAD CAD NNP 10_1101-2020_10_26_351783 143 12 ) ) -RRB- 10_1101-2020_10_26_351783 143 13 , , , 10_1101-2020_10_26_351783 143 14 type type NN 10_1101-2020_10_26_351783 143 15 2 2 CD 10_1101-2020_10_26_351783 143 16 diabetes diabetes NN 10_1101-2020_10_26_351783 143 17 , , , 10_1101-2020_10_26_351783 143 18 multiple multiple JJ 10_1101-2020_10_26_351783 143 19 sclerosis sclerosis NN 10_1101-2020_10_26_351783 143 20 ( ( -LRB- 10_1101-2020_10_26_351783 143 21 MS MS NNP 10_1101-2020_10_26_351783 143 22 ) ) -RRB- 10_1101-2020_10_26_351783 143 23 , , , 10_1101-2020_10_26_351783 143 24 rheumatoid rheumatoid NNP 10_1101-2020_10_26_351783 143 25 arthritis arthritis NN 10_1101-2020_10_26_351783 143 26 ( ( -LRB- 10_1101-2020_10_26_351783 143 27 RA RA NNP 10_1101-2020_10_26_351783 143 28 ) ) -RRB- 10_1101-2020_10_26_351783 143 29 , , , 10_1101-2020_10_26_351783 143 30 and and CC 10_1101-2020_10_26_351783 143 31 the the DT 10_1101-2020_10_26_351783 143 32 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 143 33 bowel bowel NN 10_1101-2020_10_26_351783 143 34 diseases(IBD diseases(IBD NNP 10_1101-2020_10_26_351783 143 35 ) ) -RRB- 10_1101-2020_10_26_351783 143 36 , , , 10_1101-2020_10_26_351783 143 37 ulcerative ulcerative JJ 10_1101-2020_10_26_351783 143 38 colitis colitis NN 10_1101-2020_10_26_351783 143 39 ( ( -LRB- 10_1101-2020_10_26_351783 143 40 UC UC NNP 10_1101-2020_10_26_351783 143 41 ) ) -RRB- 10_1101-2020_10_26_351783 143 42 and and CC 10_1101-2020_10_26_351783 143 43 Crohn Crohn NNP 10_1101-2020_10_26_351783 143 44 ’s ’s POS 10_1101-2020_10_26_351783 143 45 disease disease NN 10_1101-2020_10_26_351783 143 46 ( ( -LRB- 10_1101-2020_10_26_351783 143 47 CD cd NN 10_1101-2020_10_26_351783 143 48 ) ) -RRB- 10_1101-2020_10_26_351783 143 49 , , , 10_1101-2020_10_26_351783 143 50 while while IN 10_1101-2020_10_26_351783 143 51 no no DT 10_1101-2020_10_26_351783 143 52 significant significant JJ 10_1101-2020_10_26_351783 143 53 enrichments enrichment NNS 10_1101-2020_10_26_351783 143 54 were be VBD 10_1101-2020_10_26_351783 143 55 found find VBN 10_1101-2020_10_26_351783 143 56 for for IN 10_1101-2020_10_26_351783 143 57 asthma asthma NN 10_1101-2020_10_26_351783 143 58 , , , 10_1101-2020_10_26_351783 143 59 hepatitis hepatitis NNP 10_1101-2020_10_26_351783 143 60 C C NNP 10_1101-2020_10_26_351783 143 61 , , , 10_1101-2020_10_26_351783 143 62 type type NN 10_1101-2020_10_26_351783 143 63 1 1 CD 10_1101-2020_10_26_351783 143 64 diabetes diabetes NN 10_1101-2020_10_26_351783 143 65 , , , 10_1101-2020_10_26_351783 143 66 narcolepsy narcolepsy NN 10_1101-2020_10_26_351783 143 67 , , , 10_1101-2020_10_26_351783 143 68 Parkinson Parkinson NNP 10_1101-2020_10_26_351783 143 69 ’s ’s POS 10_1101-2020_10_26_351783 143 70 disease disease NN 10_1101-2020_10_26_351783 143 71 , , , 10_1101-2020_10_26_351783 143 72 or or CC 10_1101-2020_10_26_351783 143 73 for for IN 10_1101-2020_10_26_351783 143 74 any any DT 10_1101-2020_10_26_351783 143 75 psychiatric psychiatric JJ 10_1101-2020_10_26_351783 143 76 and and CC 10_1101-2020_10_26_351783 143 77 social social JJ 10_1101-2020_10_26_351783 143 78 diseases disease NNS 10_1101-2020_10_26_351783 143 79 . . . 10_1101-2020_10_26_351783 144 1 If if IN 10_1101-2020_10_26_351783 144 2 we -PRON- PRP 10_1101-2020_10_26_351783 144 3 instead instead RB 10_1101-2020_10_26_351783 144 4 ranked rank VBD 10_1101-2020_10_26_351783 144 5 methods method NNS 10_1101-2020_10_26_351783 144 6 based base VBN 10_1101-2020_10_26_351783 144 7 on on IN 10_1101-2020_10_26_351783 144 8 their -PRON- PRP$ 10_1101-2020_10_26_351783 144 9 respective respective JJ 10_1101-2020_10_26_351783 144 10 module module NN 10_1101-2020_10_26_351783 144 11 GWAS gwa VBN 10_1101-2020_10_26_351783 144 12 enrichment enrichment NN 10_1101-2020_10_26_351783 144 13 , , , 10_1101-2020_10_26_351783 144 14 Clique Clique NNP 10_1101-2020_10_26_351783 144 15 SuM sum NN 10_1101-2020_10_26_351783 144 16 showed show VBD 10_1101-2020_10_26_351783 144 17 significant significant JJ 10_1101-2020_10_26_351783 144 18 association association NN 10_1101-2020_10_26_351783 144 19 in in IN 10_1101-2020_10_26_351783 144 20 34 34 CD 10_1101-2020_10_26_351783 144 21 % % NN 10_1101-2020_10_26_351783 144 22 ( ( -LRB- 10_1101-2020_10_26_351783 144 23 16/47 16/47 CD 10_1101-2020_10_26_351783 144 24 ) ) -RRB- 10_1101-2020_10_26_351783 144 25 of of IN 10_1101-2020_10_26_351783 144 26 the the DT 10_1101-2020_10_26_351783 144 27 modules module NNS 10_1101-2020_10_26_351783 144 28 corresponding correspond VBG 10_1101-2020_10_26_351783 144 29 to to IN 10_1101-2020_10_26_351783 144 30 seven seven CD 10_1101-2020_10_26_351783 144 31 different different JJ 10_1101-2020_10_26_351783 144 32 diseases disease NNS 10_1101-2020_10_26_351783 144 33 followed follow VBN 10_1101-2020_10_26_351783 144 34 by by IN 10_1101-2020_10_26_351783 144 35 consensus consensus NN 10_1101-2020_10_26_351783 144 36 modules module NNS 10_1101-2020_10_26_351783 144 37 identified identify VBN 10_1101-2020_10_26_351783 144 38 by by IN 10_1101-2020_10_26_351783 144 39 two two CD 10_1101-2020_10_26_351783 144 40 out out IN 10_1101-2020_10_26_351783 144 41 of of IN 10_1101-2020_10_26_351783 144 42 three three CD 10_1101-2020_10_26_351783 144 43 methods method NNS 10_1101-2020_10_26_351783 144 44 . . . 10_1101-2020_10_26_351783 145 1 Lastly lastly RB 10_1101-2020_10_26_351783 145 2 , , , 10_1101-2020_10_26_351783 145 3 DIAMOnD diamond NN 10_1101-2020_10_26_351783 145 4 and and CC 10_1101-2020_10_26_351783 145 5 co- co- VBD 10_1101-2020_10_26_351783 145 6 expression expression NN 10_1101-2020_10_26_351783 145 7 - - HYPH 10_1101-2020_10_26_351783 145 8 based base VBN 10_1101-2020_10_26_351783 145 9 methods method NNS 10_1101-2020_10_26_351783 145 10 all all DT 10_1101-2020_10_26_351783 145 11 achieved achieve VBN 10_1101-2020_10_26_351783 145 12 significant significant JJ 10_1101-2020_10_26_351783 145 13 results result NNS 10_1101-2020_10_26_351783 145 14 , , , 10_1101-2020_10_26_351783 145 15 although although IN 10_1101-2020_10_26_351783 145 16 worse bad JJR 10_1101-2020_10_26_351783 145 17 than than IN 10_1101-2020_10_26_351783 145 18 Clique Clique NNP 10_1101-2020_10_26_351783 145 19 SuM. SuM. NNP 10_1101-2020_10_26_351783 146 1 Next next RB 10_1101-2020_10_26_351783 146 2 , , , 10_1101-2020_10_26_351783 146 3 we -PRON- PRP 10_1101-2020_10_26_351783 146 4 tested test VBD 10_1101-2020_10_26_351783 146 5 the the DT 10_1101-2020_10_26_351783 146 6 impact impact NN 10_1101-2020_10_26_351783 146 7 of of IN 10_1101-2020_10_26_351783 146 8 network network NN 10_1101-2020_10_26_351783 146 9 centrality centrality NN 10_1101-2020_10_26_351783 146 10 and and CC 10_1101-2020_10_26_351783 146 11 module module JJ 10_1101-2020_10_26_351783 146 12 size size NN 10_1101-2020_10_26_351783 146 13 as as IN 10_1101-2020_10_26_351783 146 14 potential potential JJ 10_1101-2020_10_26_351783 146 15 confounding confound VBG 10_1101-2020_10_26_351783 146 16 factors factor NNS 10_1101-2020_10_26_351783 146 17 of of IN 10_1101-2020_10_26_351783 146 18 the the DT 10_1101-2020_10_26_351783 146 19 applied applied JJ 10_1101-2020_10_26_351783 146 20 performance performance NN 10_1101-2020_10_26_351783 146 21 metric metric NN 10_1101-2020_10_26_351783 146 22 . . . 10_1101-2020_10_26_351783 147 1 We -PRON- PRP 10_1101-2020_10_26_351783 147 2 found find VBD 10_1101-2020_10_26_351783 147 3 a a DT 10_1101-2020_10_26_351783 147 4 significant significant JJ 10_1101-2020_10_26_351783 147 5 but but CC 10_1101-2020_10_26_351783 147 6 very very RB 10_1101-2020_10_26_351783 147 7 modest modest JJ 10_1101-2020_10_26_351783 147 8 correlation correlation NN 10_1101-2020_10_26_351783 147 9 for for IN 10_1101-2020_10_26_351783 147 10 module module JJ 10_1101-2020_10_26_351783 147 11 size size NN 10_1101-2020_10_26_351783 147 12 ( ( -LRB- 10_1101-2020_10_26_351783 147 13 Fig fig NN 10_1101-2020_10_26_351783 147 14 . . . 10_1101-2020_10_26_351783 148 1 2c 2c LS 10_1101-2020_10_26_351783 148 2 , , , 10_1101-2020_10_26_351783 148 3 Spearman Spearman NNP 10_1101-2020_10_26_351783 148 4 rho rho NN 10_1101-2020_10_26_351783 148 5 = = SYM 10_1101-2020_10_26_351783 148 6 0.165 0.165 CD 10_1101-2020_10_26_351783 148 7 , , , 10_1101-2020_10_26_351783 148 8 P p NN 10_1101-2020_10_26_351783 148 9 = = SYM 10_1101-2020_10_26_351783 148 10 2.3 2.3 CD 10_1101-2020_10_26_351783 148 11 x x SYM 10_1101-2020_10_26_351783 148 12 10 10 CD 10_1101-2020_10_26_351783 148 13 - - SYM 10_1101-2020_10_26_351783 148 14 3 3 CD 10_1101-2020_10_26_351783 148 15 ) ) -RRB- 10_1101-2020_10_26_351783 148 16 , , , 10_1101-2020_10_26_351783 148 17 and and CC 10_1101-2020_10_26_351783 148 18 a a DT 10_1101-2020_10_26_351783 148 19 non non JJ 10_1101-2020_10_26_351783 148 20 - - JJ 10_1101-2020_10_26_351783 148 21 significant significant JJ 10_1101-2020_10_26_351783 148 22 correlation correlation NN 10_1101-2020_10_26_351783 148 23 for for IN 10_1101-2020_10_26_351783 148 24 interactome interactome NN 10_1101-2020_10_26_351783 148 25 ( ( -LRB- 10_1101-2020_10_26_351783 148 26 which which WDT 10_1101-2020_10_26_351783 148 27 was be VBD 10_1101-2020_10_26_351783 148 28 not not RB 10_1101-2020_10_26_351783 148 29 certified certify VBN 10_1101-2020_10_26_351783 148 30 by by IN 10_1101-2020_10_26_351783 148 31 peer peer NN 10_1101-2020_10_26_351783 148 32 review review NN 10_1101-2020_10_26_351783 148 33 ) ) -RRB- 10_1101-2020_10_26_351783 148 34 is be VBZ 10_1101-2020_10_26_351783 148 35 the the DT 10_1101-2020_10_26_351783 148 36 author author NN 10_1101-2020_10_26_351783 148 37 / / SYM 10_1101-2020_10_26_351783 148 38 funder funder NN 10_1101-2020_10_26_351783 148 39 . . . 10_1101-2020_10_26_351783 149 1 All all DT 10_1101-2020_10_26_351783 149 2 rights right NNS 10_1101-2020_10_26_351783 149 3 reserved reserve VBD 10_1101-2020_10_26_351783 149 4 . . . 10_1101-2020_10_26_351783 150 1 No no DT 10_1101-2020_10_26_351783 150 2 reuse reuse NN 10_1101-2020_10_26_351783 150 3 allowed allow VBN 10_1101-2020_10_26_351783 150 4 without without IN 10_1101-2020_10_26_351783 150 5 permission permission NN 10_1101-2020_10_26_351783 150 6 . . . 10_1101-2020_10_26_351783 151 1 The the DT 10_1101-2020_10_26_351783 151 2 copyright copyright NN 10_1101-2020_10_26_351783 151 3 holder holder NN 10_1101-2020_10_26_351783 151 4 for for IN 10_1101-2020_10_26_351783 151 5 this this DT 10_1101-2020_10_26_351783 151 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 151 7 version version NN 10_1101-2020_10_26_351783 151 8 posted post VBD 10_1101-2020_10_26_351783 151 9 January January NNP 10_1101-2020_10_26_351783 151 10 6 6 CD 10_1101-2020_10_26_351783 151 11 , , , 10_1101-2020_10_26_351783 151 12 2021 2021 CD 10_1101-2020_10_26_351783 151 13 . . . 10_1101-2020_10_26_351783 151 14 ; ; : 10_1101-2020_10_26_351783 151 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 151 16 : : : 10_1101-2020_10_26_351783 151 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 151 18 preprint preprint NN 10_1101-2020_10_26_351783 151 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 151 20 11 11 CD 10_1101-2020_10_26_351783 151 21 centrality centrality NN 10_1101-2020_10_26_351783 151 22 ( ( -LRB- 10_1101-2020_10_26_351783 151 23 Fig fig NN 10_1101-2020_10_26_351783 151 24 . . . 10_1101-2020_10_26_351783 152 1 2b 2b NNP 10_1101-2020_10_26_351783 152 2 , , , 10_1101-2020_10_26_351783 152 3 rho rho NNP 10_1101-2020_10_26_351783 152 4 = = SYM 10_1101-2020_10_26_351783 152 5 0.068 0.068 CD 10_1101-2020_10_26_351783 152 6 , , , 10_1101-2020_10_26_351783 152 7 P p NN 10_1101-2020_10_26_351783 152 8 = = SYM 10_1101-2020_10_26_351783 152 9 0.21 0.21 CD 10_1101-2020_10_26_351783 152 10 ) ) -RRB- 10_1101-2020_10_26_351783 152 11 . . . 10_1101-2020_10_26_351783 153 1 Thus thus RB 10_1101-2020_10_26_351783 153 2 , , , 10_1101-2020_10_26_351783 153 3 it -PRON- PRP 10_1101-2020_10_26_351783 153 4 is be VBZ 10_1101-2020_10_26_351783 153 5 meaningful meaningful JJ 10_1101-2020_10_26_351783 153 6 to to TO 10_1101-2020_10_26_351783 153 7 compare compare VB 10_1101-2020_10_26_351783 153 8 results result NNS 10_1101-2020_10_26_351783 153 9 with with IN 10_1101-2020_10_26_351783 153 10 differences difference NNS 10_1101-2020_10_26_351783 153 11 in in IN 10_1101-2020_10_26_351783 153 12 those those DT 10_1101-2020_10_26_351783 153 13 module module JJ 10_1101-2020_10_26_351783 153 14 properties property NNS 10_1101-2020_10_26_351783 153 15 . . . 10_1101-2020_10_26_351783 154 1 In in IN 10_1101-2020_10_26_351783 154 2 summary summary NN 10_1101-2020_10_26_351783 154 3 , , , 10_1101-2020_10_26_351783 154 4 we -PRON- PRP 10_1101-2020_10_26_351783 154 5 found find VBD 10_1101-2020_10_26_351783 154 6 that that IN 10_1101-2020_10_26_351783 154 7 the the DT 10_1101-2020_10_26_351783 154 8 Clique Clique NNP 10_1101-2020_10_26_351783 154 9 SuM sum NN 10_1101-2020_10_26_351783 154 10 method method NN 10_1101-2020_10_26_351783 154 11 resulted result VBD 10_1101-2020_10_26_351783 154 12 in in IN 10_1101-2020_10_26_351783 154 13 the the DT 10_1101-2020_10_26_351783 154 14 highest high JJS 10_1101-2020_10_26_351783 154 15 disease disease NN 10_1101-2020_10_26_351783 154 16 enrichment enrichment NN 10_1101-2020_10_26_351783 154 17 for for IN 10_1101-2020_10_26_351783 154 18 most most JJS 10_1101-2020_10_26_351783 154 19 diseases disease NNS 10_1101-2020_10_26_351783 154 20 , , , 10_1101-2020_10_26_351783 154 21 while while IN 10_1101-2020_10_26_351783 154 22 not not RB 10_1101-2020_10_26_351783 154 23 producing produce VBG 10_1101-2020_10_26_351783 154 24 significant significant JJ 10_1101-2020_10_26_351783 154 25 modules module NNS 10_1101-2020_10_26_351783 154 26 for for IN 10_1101-2020_10_26_351783 154 27 others other NNS 10_1101-2020_10_26_351783 154 28 , , , 10_1101-2020_10_26_351783 154 29 such such JJ 10_1101-2020_10_26_351783 154 30 as as IN 10_1101-2020_10_26_351783 154 31 type type NN 10_1101-2020_10_26_351783 154 32 2 2 CD 10_1101-2020_10_26_351783 154 33 diabetes diabetes NN 10_1101-2020_10_26_351783 154 34 , , , 10_1101-2020_10_26_351783 154 35 where where WRB 10_1101-2020_10_26_351783 154 36 co co NN 10_1101-2020_10_26_351783 154 37 - - JJ 10_1101-2020_10_26_351783 154 38 expression expression NN 10_1101-2020_10_26_351783 154 39 - - HYPH 10_1101-2020_10_26_351783 154 40 based base VBN 10_1101-2020_10_26_351783 154 41 methods method NNS 10_1101-2020_10_26_351783 154 42 and and CC 10_1101-2020_10_26_351783 154 43 DIAMOnD diamond NN 10_1101-2020_10_26_351783 154 44 scored score VBD 10_1101-2020_10_26_351783 154 45 best well RBS 10_1101-2020_10_26_351783 154 46 . . . 10_1101-2020_10_26_351783 155 1 In in IN 10_1101-2020_10_26_351783 155 2 general general JJ 10_1101-2020_10_26_351783 155 3 , , , 10_1101-2020_10_26_351783 155 4 we -PRON- PRP 10_1101-2020_10_26_351783 155 5 observed observe VBD 10_1101-2020_10_26_351783 155 6 stronger strong JJR 10_1101-2020_10_26_351783 155 7 enrichments enrichment NNS 10_1101-2020_10_26_351783 155 8 for for IN 10_1101-2020_10_26_351783 155 9 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 155 10 diseases disease NNS 10_1101-2020_10_26_351783 155 11 and and CC 10_1101-2020_10_26_351783 155 12 weaker weak JJR 10_1101-2020_10_26_351783 155 13 results result NNS 10_1101-2020_10_26_351783 155 14 for for IN 10_1101-2020_10_26_351783 155 15 psychiatric psychiatric JJ 10_1101-2020_10_26_351783 155 16 and and CC 10_1101-2020_10_26_351783 155 17 social social JJ 10_1101-2020_10_26_351783 155 18 diseases disease NNS 10_1101-2020_10_26_351783 155 19 . . . 10_1101-2020_10_26_351783 156 1 Considering consider VBG 10_1101-2020_10_26_351783 156 2 that that IN 10_1101-2020_10_26_351783 156 3 the the DT 10_1101-2020_10_26_351783 156 4 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 156 5 modules module NNS 10_1101-2020_10_26_351783 156 6 showed show VBD 10_1101-2020_10_26_351783 156 7 that that IN 10_1101-2020_10_26_351783 156 8 Clique Clique NNP 10_1101-2020_10_26_351783 156 9 SuM sum NN 10_1101-2020_10_26_351783 156 10 was be VBD 10_1101-2020_10_26_351783 156 11 the the DT 10_1101-2020_10_26_351783 156 12 best good JJS 10_1101-2020_10_26_351783 156 13 performing performing NN 10_1101-2020_10_26_351783 156 14 method method NN 10_1101-2020_10_26_351783 156 15 and and CC 10_1101-2020_10_26_351783 156 16 that that IN 10_1101-2020_10_26_351783 156 17 the the DT 10_1101-2020_10_26_351783 156 18 cardiovascular cardiovascular JJ 10_1101-2020_10_26_351783 156 19 and and CC 10_1101-2020_10_26_351783 156 20 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 156 21 diseases disease NNS 10_1101-2020_10_26_351783 156 22 were be VBD 10_1101-2020_10_26_351783 156 23 the the DT 10_1101-2020_10_26_351783 156 24 most most RBS 10_1101-2020_10_26_351783 156 25 enriched enrich VBN 10_1101-2020_10_26_351783 156 26 within within IN 10_1101-2020_10_26_351783 156 27 the the DT 10_1101-2020_10_26_351783 156 28 Clique Clique NNP 10_1101-2020_10_26_351783 156 29 SuM sum NN 10_1101-2020_10_26_351783 156 30 modules module NNS 10_1101-2020_10_26_351783 156 31 , , , 10_1101-2020_10_26_351783 156 32 we -PRON- PRP 10_1101-2020_10_26_351783 156 33 wanted want VBD 10_1101-2020_10_26_351783 156 34 to to TO 10_1101-2020_10_26_351783 156 35 test test VB 10_1101-2020_10_26_351783 156 36 whether whether IN 10_1101-2020_10_26_351783 156 37 this this DT 10_1101-2020_10_26_351783 156 38 was be VBD 10_1101-2020_10_26_351783 156 39 true true JJ 10_1101-2020_10_26_351783 156 40 for for IN 10_1101-2020_10_26_351783 156 41 methylomic methylomic JJ 10_1101-2020_10_26_351783 156 42 data datum NNS 10_1101-2020_10_26_351783 156 43 as as RB 10_1101-2020_10_26_351783 156 44 well well RB 10_1101-2020_10_26_351783 156 45 . . . 10_1101-2020_10_26_351783 157 1 A a DT 10_1101-2020_10_26_351783 157 2 benchmark benchmark NN 10_1101-2020_10_26_351783 157 3 comparing compare VBG 10_1101-2020_10_26_351783 157 4 72 72 CD 10_1101-2020_10_26_351783 157 5 methylation methylation NN 10_1101-2020_10_26_351783 157 6 - - HYPH 10_1101-2020_10_26_351783 157 7 based base VBN 10_1101-2020_10_26_351783 157 8 disease disease NN 10_1101-2020_10_26_351783 157 9 modules module NNS 10_1101-2020_10_26_351783 157 10 from from IN 10_1101-2020_10_26_351783 157 11 six six CD 10_1101-2020_10_26_351783 157 12 different different JJ 10_1101-2020_10_26_351783 157 13 diseases disease NNS 10_1101-2020_10_26_351783 157 14 using use VBG 10_1101-2020_10_26_351783 157 15 GWAS GWAS NNP 10_1101-2020_10_26_351783 157 16 . . . 10_1101-2020_10_26_351783 158 1 Following follow VBG 10_1101-2020_10_26_351783 158 2 the the DT 10_1101-2020_10_26_351783 158 3 same same JJ 10_1101-2020_10_26_351783 158 4 logic logic NN 10_1101-2020_10_26_351783 158 5 of of IN 10_1101-2020_10_26_351783 158 6 the the DT 10_1101-2020_10_26_351783 158 7 transcriptomic transcriptomic NNP 10_1101-2020_10_26_351783 158 8 benchmark benchmark NN 10_1101-2020_10_26_351783 158 9 , , , 10_1101-2020_10_26_351783 158 10 we -PRON- PRP 10_1101-2020_10_26_351783 158 11 performed perform VBD 10_1101-2020_10_26_351783 158 12 a a DT 10_1101-2020_10_26_351783 158 13 similar similar JJ 10_1101-2020_10_26_351783 158 14 benchmark benchmark JJ 10_1101-2020_10_26_351783 158 15 study study NN 10_1101-2020_10_26_351783 158 16 for for IN 10_1101-2020_10_26_351783 158 17 methylation methylation NN 10_1101-2020_10_26_351783 158 18 modules module NNS 10_1101-2020_10_26_351783 158 19 . . . 10_1101-2020_10_26_351783 159 1 We -PRON- PRP 10_1101-2020_10_26_351783 159 2 collected collect VBD 10_1101-2020_10_26_351783 159 3 ten ten JJ 10_1101-2020_10_26_351783 159 4 datasets dataset NNS 10_1101-2020_10_26_351783 159 5 from from IN 10_1101-2020_10_26_351783 159 6 three three CD 10_1101-2020_10_26_351783 159 7 different different JJ 10_1101-2020_10_26_351783 159 8 disease disease NN 10_1101-2020_10_26_351783 159 9 categories category NNS 10_1101-2020_10_26_351783 159 10 , , , 10_1101-2020_10_26_351783 159 11 including include VBG 10_1101-2020_10_26_351783 159 12 six six CD 10_1101-2020_10_26_351783 159 13 complex complex JJ 10_1101-2020_10_26_351783 159 14 diseases disease NNS 10_1101-2020_10_26_351783 159 15 , , , 10_1101-2020_10_26_351783 159 16 and and CC 10_1101-2020_10_26_351783 159 17 ran run VBD 10_1101-2020_10_26_351783 159 18 the the DT 10_1101-2020_10_26_351783 159 19 eight eight CD 10_1101-2020_10_26_351783 159 20 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 159 21 methods method NNS 10_1101-2020_10_26_351783 159 22 on on IN 10_1101-2020_10_26_351783 159 23 them -PRON- PRP 10_1101-2020_10_26_351783 159 24 ( ( -LRB- 10_1101-2020_10_26_351783 159 25 Fig fig NN 10_1101-2020_10_26_351783 159 26 . . . 10_1101-2020_10_26_351783 160 1 1a 1a LS 10_1101-2020_10_26_351783 160 2 ) ) -RRB- 10_1101-2020_10_26_351783 160 3 . . . 10_1101-2020_10_26_351783 161 1 In in IN 10_1101-2020_10_26_351783 161 2 addition addition NN 10_1101-2020_10_26_351783 161 3 , , , 10_1101-2020_10_26_351783 161 4 we -PRON- PRP 10_1101-2020_10_26_351783 161 5 constructed construct VBD 10_1101-2020_10_26_351783 161 6 consensus consensus NN 10_1101-2020_10_26_351783 161 7 modules module NNS 10_1101-2020_10_26_351783 161 8 for for IN 10_1101-2020_10_26_351783 161 9 each each DT 10_1101-2020_10_26_351783 161 10 of of IN 10_1101-2020_10_26_351783 161 11 the the DT 10_1101-2020_10_26_351783 161 12 datasets dataset NNS 10_1101-2020_10_26_351783 161 13 . . . 10_1101-2020_10_26_351783 162 1 Modules module NNS 10_1101-2020_10_26_351783 162 2 were be VBD 10_1101-2020_10_26_351783 162 3 then then RB 10_1101-2020_10_26_351783 162 4 tested test VBN 10_1101-2020_10_26_351783 162 5 for for IN 10_1101-2020_10_26_351783 162 6 GWAS GWAS NNP 10_1101-2020_10_26_351783 162 7 enrichment enrichment NN 10_1101-2020_10_26_351783 162 8 using use VBG 10_1101-2020_10_26_351783 162 9 Pascal Pascal NNP 10_1101-2020_10_26_351783 162 10 . . . 10_1101-2020_10_26_351783 163 1 Inspecting inspect VBG 10_1101-2020_10_26_351783 163 2 the the DT 10_1101-2020_10_26_351783 163 3 overall overall JJ 10_1101-2020_10_26_351783 163 4 performance performance NN 10_1101-2020_10_26_351783 163 5 , , , 10_1101-2020_10_26_351783 163 6 we -PRON- PRP 10_1101-2020_10_26_351783 163 7 found find VBD 10_1101-2020_10_26_351783 163 8 nine nine CD 10_1101-2020_10_26_351783 163 9 single single JJ 10_1101-2020_10_26_351783 163 10 - - HYPH 10_1101-2020_10_26_351783 163 11 method method NN 10_1101-2020_10_26_351783 163 12 modules module NNS 10_1101-2020_10_26_351783 163 13 with with IN 10_1101-2020_10_26_351783 163 14 a a DT 10_1101-2020_10_26_351783 163 15 significant significant JJ 10_1101-2020_10_26_351783 163 16 GWAS GWAS NNP 10_1101-2020_10_26_351783 163 17 enrichment enrichment NN 10_1101-2020_10_26_351783 163 18 ( ( -LRB- 10_1101-2020_10_26_351783 163 19 9/72 9/72 CD 10_1101-2020_10_26_351783 163 20 , , , 10_1101-2020_10_26_351783 163 21 11.8 11.8 CD 10_1101-2020_10_26_351783 163 22 % % NN 10_1101-2020_10_26_351783 163 23 ) ) -RRB- 10_1101-2020_10_26_351783 163 24 . . . 10_1101-2020_10_26_351783 164 1 Though though IN 10_1101-2020_10_26_351783 164 2 this this DT 10_1101-2020_10_26_351783 164 3 might may MD 10_1101-2020_10_26_351783 164 4 be be VB 10_1101-2020_10_26_351783 164 5 due due IN 10_1101-2020_10_26_351783 164 6 to to IN 10_1101-2020_10_26_351783 164 7 disease disease NN 10_1101-2020_10_26_351783 164 8 and and CC 10_1101-2020_10_26_351783 164 9 cell cell NN 10_1101-2020_10_26_351783 164 10 type type NN 10_1101-2020_10_26_351783 164 11 heterogeneity heterogeneity NN 10_1101-2020_10_26_351783 164 12 , , , 10_1101-2020_10_26_351783 164 13 the the DT 10_1101-2020_10_26_351783 164 14 enrichment enrichment NN 10_1101-2020_10_26_351783 164 15 is be VBZ 10_1101-2020_10_26_351783 164 16 more more JJR 10_1101-2020_10_26_351783 164 17 than than IN 10_1101-2020_10_26_351783 164 18 expected expect VBN 10_1101-2020_10_26_351783 164 19 by by IN 10_1101-2020_10_26_351783 164 20 chance chance NN 10_1101-2020_10_26_351783 164 21 ( ( -LRB- 10_1101-2020_10_26_351783 164 22 P=9.6x P=9.6x NNP 10_1101-2020_10_26_351783 164 23 10 10 CD 10_1101-2020_10_26_351783 164 24 - - SYM 10_1101-2020_10_26_351783 164 25 3 3 CD 10_1101-2020_10_26_351783 164 26 ) ) -RRB- 10_1101-2020_10_26_351783 164 27 . . . 10_1101-2020_10_26_351783 165 1 Interestingly interestingly RB 10_1101-2020_10_26_351783 165 2 , , , 10_1101-2020_10_26_351783 165 3 the the DT 10_1101-2020_10_26_351783 165 4 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 165 5 diseases disease NNS 10_1101-2020_10_26_351783 165 6 such such JJ 10_1101-2020_10_26_351783 165 7 as as IN 10_1101-2020_10_26_351783 165 8 MS MS NNP 10_1101-2020_10_26_351783 165 9 and and CC 10_1101-2020_10_26_351783 165 10 UC UC NNP 10_1101-2020_10_26_351783 165 11 showed show VBD 10_1101-2020_10_26_351783 165 12 a a DT 10_1101-2020_10_26_351783 165 13 more more RBR 10_1101-2020_10_26_351783 165 14 significant significant JJ 10_1101-2020_10_26_351783 165 15 GWAS GWAS NNP 10_1101-2020_10_26_351783 165 16 enrichment enrichment NN 10_1101-2020_10_26_351783 165 17 Considering consider VBG 10_1101-2020_10_26_351783 165 18 that that IN 10_1101-2020_10_26_351783 165 19 the the DT 10_1101-2020_10_26_351783 165 20 evaluation evaluation NN 10_1101-2020_10_26_351783 165 21 of of IN 10_1101-2020_10_26_351783 165 22 module module JJ 10_1101-2020_10_26_351783 165 23 performance performance NN 10_1101-2020_10_26_351783 165 24 by by IN 10_1101-2020_10_26_351783 165 25 GWAS GWAS NNP 10_1101-2020_10_26_351783 165 26 enrichment enrichment NN 10_1101-2020_10_26_351783 165 27 may may MD 10_1101-2020_10_26_351783 165 28 be be VB 10_1101-2020_10_26_351783 165 29 biased biased JJ 10_1101-2020_10_26_351783 165 30 due due IN 10_1101-2020_10_26_351783 165 31 to to IN 10_1101-2020_10_26_351783 165 32 differences difference NNS 10_1101-2020_10_26_351783 165 33 in in IN 10_1101-2020_10_26_351783 165 34 module module JJ 10_1101-2020_10_26_351783 165 35 sizes size NNS 10_1101-2020_10_26_351783 165 36 and and CC 10_1101-2020_10_26_351783 165 37 interactome interactome JJ 10_1101-2020_10_26_351783 165 38 centrality centrality NN 10_1101-2020_10_26_351783 165 39 , , , 10_1101-2020_10_26_351783 165 40 we -PRON- PRP 10_1101-2020_10_26_351783 165 41 again again RB 10_1101-2020_10_26_351783 165 42 assessed assess VBD 10_1101-2020_10_26_351783 165 43 the the DT 10_1101-2020_10_26_351783 165 44 correlation correlation NN 10_1101-2020_10_26_351783 165 45 between between IN 10_1101-2020_10_26_351783 165 46 these these DT 10_1101-2020_10_26_351783 165 47 values value NNS 10_1101-2020_10_26_351783 165 48 . . . 10_1101-2020_10_26_351783 166 1 We -PRON- PRP 10_1101-2020_10_26_351783 166 2 found find VBD 10_1101-2020_10_26_351783 166 3 a a DT 10_1101-2020_10_26_351783 166 4 significant significant JJ 10_1101-2020_10_26_351783 166 5 correlation correlation NN 10_1101-2020_10_26_351783 166 6 between between IN 10_1101-2020_10_26_351783 166 7 GWAS GWAS NNP 10_1101-2020_10_26_351783 166 8 enrichment enrichment NN 10_1101-2020_10_26_351783 166 9 and and CC 10_1101-2020_10_26_351783 166 10 module module JJ 10_1101-2020_10_26_351783 166 11 size size NN 10_1101-2020_10_26_351783 166 12 ( ( -LRB- 10_1101-2020_10_26_351783 166 13 Fig fig NN 10_1101-2020_10_26_351783 166 14 . . . 10_1101-2020_10_26_351783 167 1 3c 3c LS 10_1101-2020_10_26_351783 167 2 , , , 10_1101-2020_10_26_351783 167 3 rho rho NN 10_1101-2020_10_26_351783 167 4 = = SYM 10_1101-2020_10_26_351783 167 5 0.235 0.235 CD 10_1101-2020_10_26_351783 167 6 , , , 10_1101-2020_10_26_351783 167 7 P p NN 10_1101-2020_10_26_351783 167 8 = = SYM 10_1101-2020_10_26_351783 167 9 0.046 0.046 CD 10_1101-2020_10_26_351783 167 10 ) ) -RRB- 10_1101-2020_10_26_351783 167 11 and and CC 10_1101-2020_10_26_351783 167 12 a a DT 10_1101-2020_10_26_351783 167 13 non non JJ 10_1101-2020_10_26_351783 167 14 - - JJ 10_1101-2020_10_26_351783 167 15 significant significant JJ 10_1101-2020_10_26_351783 167 16 correlation correlation NN 10_1101-2020_10_26_351783 167 17 between between IN 10_1101-2020_10_26_351783 167 18 GWAS GWAS NNP 10_1101-2020_10_26_351783 167 19 enrichment enrichment NN 10_1101-2020_10_26_351783 167 20 and and CC 10_1101-2020_10_26_351783 167 21 interactome interactome JJ 10_1101-2020_10_26_351783 167 22 centrality centrality NN 10_1101-2020_10_26_351783 167 23 ( ( -LRB- 10_1101-2020_10_26_351783 167 24 Fig fig NN 10_1101-2020_10_26_351783 167 25 . . . 10_1101-2020_10_26_351783 168 1 3b 3b LS 10_1101-2020_10_26_351783 168 2 , , , 10_1101-2020_10_26_351783 168 3 rho rho NNP 10_1101-2020_10_26_351783 168 4 = = SYM 10_1101-2020_10_26_351783 168 5 0.190 0.190 CD 10_1101-2020_10_26_351783 168 6 , , , 10_1101-2020_10_26_351783 168 7 P p NN 10_1101-2020_10_26_351783 168 8 = = SYM 10_1101-2020_10_26_351783 168 9 0.109 0.109 CD 10_1101-2020_10_26_351783 168 10 ) ) -RRB- 10_1101-2020_10_26_351783 168 11 . . . 10_1101-2020_10_26_351783 169 1 We -PRON- PRP 10_1101-2020_10_26_351783 169 2 found find VBD 10_1101-2020_10_26_351783 169 3 that that IN 10_1101-2020_10_26_351783 169 4 12.5 12.5 CD 10_1101-2020_10_26_351783 169 5 % % NN 10_1101-2020_10_26_351783 169 6 of of IN 10_1101-2020_10_26_351783 169 7 the the DT 10_1101-2020_10_26_351783 169 8 disease disease NN 10_1101-2020_10_26_351783 169 9 - - HYPH 10_1101-2020_10_26_351783 169 10 method method NN 10_1101-2020_10_26_351783 169 11 combinations combination NNS 10_1101-2020_10_26_351783 169 12 yielded yield VBD 10_1101-2020_10_26_351783 169 13 significant significant JJ 10_1101-2020_10_26_351783 169 14 GWAS GWAS NNP 10_1101-2020_10_26_351783 169 15 enrichment enrichment NN 10_1101-2020_10_26_351783 169 16 , , , 10_1101-2020_10_26_351783 169 17 which which WDT 10_1101-2020_10_26_351783 169 18 is be VBZ 10_1101-2020_10_26_351783 169 19 more more JJR 10_1101-2020_10_26_351783 169 20 than than IN 10_1101-2020_10_26_351783 169 21 expected expect VBN 10_1101-2020_10_26_351783 169 22 from from IN 10_1101-2020_10_26_351783 169 23 an an DT 10_1101-2020_10_26_351783 169 24 independent independent JJ 10_1101-2020_10_26_351783 169 25 random random JJ 10_1101-2020_10_26_351783 169 26 selection selection NN 10_1101-2020_10_26_351783 169 27 of of IN 10_1101-2020_10_26_351783 169 28 modules module NNS 10_1101-2020_10_26_351783 169 29 ( ( -LRB- 10_1101-2020_10_26_351783 169 30 Fisher Fisher NNP 10_1101-2020_10_26_351783 169 31 ’s ’s POS 10_1101-2020_10_26_351783 169 32 exact exact JJ 10_1101-2020_10_26_351783 169 33 test test NN 10_1101-2020_10_26_351783 169 34 P p NN 10_1101-2020_10_26_351783 169 35 = = SYM 10_1101-2020_10_26_351783 169 36 0.031 0.031 CD 10_1101-2020_10_26_351783 169 37 , , , 10_1101-2020_10_26_351783 169 38 n n CC 10_1101-2020_10_26_351783 169 39 = = SYM 10_1101-2020_10_26_351783 169 40 6 6 CD 10_1101-2020_10_26_351783 169 41 ) ) -RRB- 10_1101-2020_10_26_351783 169 42 . . . 10_1101-2020_10_26_351783 170 1 The the DT 10_1101-2020_10_26_351783 170 2 highly highly RB 10_1101-2020_10_26_351783 170 3 enriched enriched JJ 10_1101-2020_10_26_351783 170 4 disease disease NN 10_1101-2020_10_26_351783 170 5 modules module NNS 10_1101-2020_10_26_351783 170 6 belong belong VBP 10_1101-2020_10_26_351783 170 7 to to IN 10_1101-2020_10_26_351783 170 8 MS MS NNP 10_1101-2020_10_26_351783 170 9 , , , 10_1101-2020_10_26_351783 170 10 UC UC NNP 10_1101-2020_10_26_351783 170 11 and and CC 10_1101-2020_10_26_351783 170 12 CD CD NNP 10_1101-2020_10_26_351783 170 13 . . . 10_1101-2020_10_26_351783 171 1 Two two CD 10_1101-2020_10_26_351783 171 2 out out IN 10_1101-2020_10_26_351783 171 3 of of IN 10_1101-2020_10_26_351783 171 4 the the DT 10_1101-2020_10_26_351783 171 5 six six CD 10_1101-2020_10_26_351783 171 6 diseases disease NNS 10_1101-2020_10_26_351783 171 7 showed show VBD 10_1101-2020_10_26_351783 171 8 significant significant JJ 10_1101-2020_10_26_351783 171 9 GWAS GWAS NNP 10_1101-2020_10_26_351783 171 10 ( ( -LRB- 10_1101-2020_10_26_351783 171 11 which which WDT 10_1101-2020_10_26_351783 171 12 was be VBD 10_1101-2020_10_26_351783 171 13 not not RB 10_1101-2020_10_26_351783 171 14 certified certify VBN 10_1101-2020_10_26_351783 171 15 by by IN 10_1101-2020_10_26_351783 171 16 peer peer NN 10_1101-2020_10_26_351783 171 17 review review NN 10_1101-2020_10_26_351783 171 18 ) ) -RRB- 10_1101-2020_10_26_351783 171 19 is be VBZ 10_1101-2020_10_26_351783 171 20 the the DT 10_1101-2020_10_26_351783 171 21 author author NN 10_1101-2020_10_26_351783 171 22 / / SYM 10_1101-2020_10_26_351783 171 23 funder funder NN 10_1101-2020_10_26_351783 171 24 . . . 10_1101-2020_10_26_351783 172 1 All all DT 10_1101-2020_10_26_351783 172 2 rights right NNS 10_1101-2020_10_26_351783 172 3 reserved reserve VBD 10_1101-2020_10_26_351783 172 4 . . . 10_1101-2020_10_26_351783 173 1 No no DT 10_1101-2020_10_26_351783 173 2 reuse reuse NN 10_1101-2020_10_26_351783 173 3 allowed allow VBN 10_1101-2020_10_26_351783 173 4 without without IN 10_1101-2020_10_26_351783 173 5 permission permission NN 10_1101-2020_10_26_351783 173 6 . . . 10_1101-2020_10_26_351783 174 1 The the DT 10_1101-2020_10_26_351783 174 2 copyright copyright NN 10_1101-2020_10_26_351783 174 3 holder holder NN 10_1101-2020_10_26_351783 174 4 for for IN 10_1101-2020_10_26_351783 174 5 this this DT 10_1101-2020_10_26_351783 174 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 174 7 version version NN 10_1101-2020_10_26_351783 174 8 posted post VBD 10_1101-2020_10_26_351783 174 9 January January NNP 10_1101-2020_10_26_351783 174 10 6 6 CD 10_1101-2020_10_26_351783 174 11 , , , 10_1101-2020_10_26_351783 174 12 2021 2021 CD 10_1101-2020_10_26_351783 174 13 . . . 10_1101-2020_10_26_351783 174 14 ; ; : 10_1101-2020_10_26_351783 174 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 174 16 : : : 10_1101-2020_10_26_351783 174 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 174 18 preprint preprint NN 10_1101-2020_10_26_351783 174 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 174 20 12 12 CD 10_1101-2020_10_26_351783 174 21 enrichment enrichment NN 10_1101-2020_10_26_351783 174 22 by by IN 10_1101-2020_10_26_351783 174 23 using use VBG 10_1101-2020_10_26_351783 174 24 the the DT 10_1101-2020_10_26_351783 174 25 Clique Clique NNP 10_1101-2020_10_26_351783 174 26 SuM sum NN 10_1101-2020_10_26_351783 174 27 modules module NNS 10_1101-2020_10_26_351783 174 28 ( ( -LRB- 10_1101-2020_10_26_351783 174 29 P p NN 10_1101-2020_10_26_351783 174 30 = = SYM 10_1101-2020_10_26_351783 174 31 0.032 0.032 CD 10_1101-2020_10_26_351783 174 32 ) ) -RRB- 10_1101-2020_10_26_351783 174 33 . . . 10_1101-2020_10_26_351783 175 1 In in IN 10_1101-2020_10_26_351783 175 2 summary summary NN 10_1101-2020_10_26_351783 175 3 , , , 10_1101-2020_10_26_351783 175 4 Clique Clique NNP 10_1101-2020_10_26_351783 175 5 SuM sum NN 10_1101-2020_10_26_351783 175 6 method method NN 10_1101-2020_10_26_351783 175 7 resulted result VBD 10_1101-2020_10_26_351783 175 8 in in IN 10_1101-2020_10_26_351783 175 9 a a DT 10_1101-2020_10_26_351783 175 10 more more RBR 10_1101-2020_10_26_351783 175 11 significant significant JJ 10_1101-2020_10_26_351783 175 12 GWAS GWAS NNP 10_1101-2020_10_26_351783 175 13 enrichment enrichment NN 10_1101-2020_10_26_351783 175 14 for for IN 10_1101-2020_10_26_351783 175 15 most most JJS 10_1101-2020_10_26_351783 175 16 diseases disease NNS 10_1101-2020_10_26_351783 175 17 also also RB 10_1101-2020_10_26_351783 175 18 for for IN 10_1101-2020_10_26_351783 175 19 the the DT 10_1101-2020_10_26_351783 175 20 methylomic methylomic JJ 10_1101-2020_10_26_351783 175 21 benchmark benchmark NN 10_1101-2020_10_26_351783 175 22 . . . 10_1101-2020_10_26_351783 176 1 Multi multi JJ 10_1101-2020_10_26_351783 176 2 - - HYPH 10_1101-2020_10_26_351783 176 3 omics omics NNP 10_1101-2020_10_26_351783 176 4 approach approach NN 10_1101-2020_10_26_351783 176 5 revealed reveal VBD 10_1101-2020_10_26_351783 176 6 a a DT 10_1101-2020_10_26_351783 176 7 module module NN 10_1101-2020_10_26_351783 176 8 enriched enrich VBN 10_1101-2020_10_26_351783 176 9 for for IN 10_1101-2020_10_26_351783 176 10 MS MS NNP 10_1101-2020_10_26_351783 176 11 - - HYPH 10_1101-2020_10_26_351783 176 12 associated associate VBN 10_1101-2020_10_26_351783 176 13 genes gene NNS 10_1101-2020_10_26_351783 176 14 . . . 10_1101-2020_10_26_351783 177 1 Considering consider VBG 10_1101-2020_10_26_351783 177 2 genomic genomic JJ 10_1101-2020_10_26_351783 177 3 concordance concordance NN 10_1101-2020_10_26_351783 177 4 as as IN 10_1101-2020_10_26_351783 177 5 the the DT 10_1101-2020_10_26_351783 177 6 guidance guidance NN 10_1101-2020_10_26_351783 177 7 principle principle NN 10_1101-2020_10_26_351783 177 8 for for IN 10_1101-2020_10_26_351783 177 9 the the DT 10_1101-2020_10_26_351783 177 10 modules module NNS 10_1101-2020_10_26_351783 177 11 that that WDT 10_1101-2020_10_26_351783 177 12 show show VBP 10_1101-2020_10_26_351783 177 13 enrichment enrichment NN 10_1101-2020_10_26_351783 177 14 for for IN 10_1101-2020_10_26_351783 177 15 GWAS GWAS NNP 10_1101-2020_10_26_351783 177 16 SNPs snp NNS 10_1101-2020_10_26_351783 177 17 , , , 10_1101-2020_10_26_351783 177 18 differentially differentially RB 10_1101-2020_10_26_351783 177 19 methylated methylate VBN 10_1101-2020_10_26_351783 177 20 genes gene NNS 10_1101-2020_10_26_351783 177 21 and and CC 10_1101-2020_10_26_351783 177 22 differentially differentially RB 10_1101-2020_10_26_351783 177 23 expressed express VBD 10_1101-2020_10_26_351783 177 24 genes gene NNS 10_1101-2020_10_26_351783 177 25 , , , 10_1101-2020_10_26_351783 177 26 we -PRON- PRP 10_1101-2020_10_26_351783 177 27 further further RB 10_1101-2020_10_26_351783 177 28 wanted want VBD 10_1101-2020_10_26_351783 177 29 to to TO 10_1101-2020_10_26_351783 177 30 evaluate evaluate VB 10_1101-2020_10_26_351783 177 31 multiple multiple JJ 10_1101-2020_10_26_351783 177 32 datasets dataset NNS 10_1101-2020_10_26_351783 177 33 of of IN 10_1101-2020_10_26_351783 177 34 one one CD 10_1101-2020_10_26_351783 177 35 specific specific JJ 10_1101-2020_10_26_351783 177 36 disease disease NN 10_1101-2020_10_26_351783 177 37 , , , 10_1101-2020_10_26_351783 177 38 i.e. i.e. FW 10_1101-2020_10_26_351783 177 39 , , , 10_1101-2020_10_26_351783 177 40 MS MS NNP 10_1101-2020_10_26_351783 177 41 . . . 10_1101-2020_10_26_351783 177 42 We -PRON- PRP 10_1101-2020_10_26_351783 177 43 compiled compile VBD 10_1101-2020_10_26_351783 177 44 11 11 CD 10_1101-2020_10_26_351783 177 45 MS MS NNP 10_1101-2020_10_26_351783 177 46 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 177 47 datasets dataset NNS 10_1101-2020_10_26_351783 177 48 and and CC 10_1101-2020_10_26_351783 177 49 nine nine CD 10_1101-2020_10_26_351783 177 50 methylation methylation NN 10_1101-2020_10_26_351783 177 51 ( ( -LRB- 10_1101-2020_10_26_351783 177 52 Supplementary Supplementary NNP 10_1101-2020_10_26_351783 177 53 Table Table NNP 10_1101-2020_10_26_351783 177 54 2 2 CD 10_1101-2020_10_26_351783 177 55 ) ) -RRB- 10_1101-2020_10_26_351783 177 56 comparisons comparison NNS 10_1101-2020_10_26_351783 177 57 from from IN 10_1101-2020_10_26_351783 177 58 GEO GEO NNP 10_1101-2020_10_26_351783 177 59 which which WDT 10_1101-2020_10_26_351783 177 60 satisfy satisfy VBP 10_1101-2020_10_26_351783 177 61 the the DT 10_1101-2020_10_26_351783 177 62 pre pre VBN 10_1101-2020_10_26_351783 177 63 - - JJ 10_1101-2020_10_26_351783 177 64 defined define VBN 10_1101-2020_10_26_351783 177 65 dataset dataset NN 10_1101-2020_10_26_351783 177 66 criteria criterion NNS 10_1101-2020_10_26_351783 177 67 ( ( -LRB- 10_1101-2020_10_26_351783 177 68 see see VB 10_1101-2020_10_26_351783 177 69 Methods Methods NNP 10_1101-2020_10_26_351783 177 70 ) ) -RRB- 10_1101-2020_10_26_351783 177 71 . . . 10_1101-2020_10_26_351783 178 1 For for IN 10_1101-2020_10_26_351783 178 2 each each DT 10_1101-2020_10_26_351783 178 3 dataset dataset NN 10_1101-2020_10_26_351783 178 4 we -PRON- PRP 10_1101-2020_10_26_351783 178 5 implemented implement VBD 10_1101-2020_10_26_351783 178 6 the the DT 10_1101-2020_10_26_351783 178 7 pipeline pipeline NN 10_1101-2020_10_26_351783 178 8 for for IN 10_1101-2020_10_26_351783 178 9 module module JJ 10_1101-2020_10_26_351783 178 10 identification identification NN 10_1101-2020_10_26_351783 178 11 and and CC 10_1101-2020_10_26_351783 178 12 scoring score VBG 10_1101-2020_10_26_351783 178 13 shown show VBN 10_1101-2020_10_26_351783 178 14 in in IN 10_1101-2020_10_26_351783 178 15 Fig Fig NNP 10_1101-2020_10_26_351783 178 16 . . . 10_1101-2020_10_26_351783 179 1 1b 1b CD 10_1101-2020_10_26_351783 179 2 . . . 10_1101-2020_10_26_351783 180 1 We -PRON- PRP 10_1101-2020_10_26_351783 180 2 evaluated evaluate VBD 10_1101-2020_10_26_351783 180 3 each each DT 10_1101-2020_10_26_351783 180 4 module module NN 10_1101-2020_10_26_351783 180 5 using use VBG 10_1101-2020_10_26_351783 180 6 MS MS NNP 10_1101-2020_10_26_351783 180 7 SNP SNP NNP 10_1101-2020_10_26_351783 180 8 enrichment enrichment NN 10_1101-2020_10_26_351783 180 9 analysis analysis NN 10_1101-2020_10_26_351783 180 10 and and CC 10_1101-2020_10_26_351783 180 11 selected select VBD 10_1101-2020_10_26_351783 180 12 the the DT 10_1101-2020_10_26_351783 180 13 most most RBS 10_1101-2020_10_26_351783 180 14 enriched enriched JJ 10_1101-2020_10_26_351783 180 15 modules module NNS 10_1101-2020_10_26_351783 180 16 per per IN 10_1101-2020_10_26_351783 180 17 omic omic JJ 10_1101-2020_10_26_351783 180 18 from from IN 10_1101-2020_10_26_351783 180 19 this this DT 10_1101-2020_10_26_351783 180 20 metric metric NN 10_1101-2020_10_26_351783 180 21 . . . 10_1101-2020_10_26_351783 181 1 This this DT 10_1101-2020_10_26_351783 181 2 analysis analysis NN 10_1101-2020_10_26_351783 181 3 again again RB 10_1101-2020_10_26_351783 181 4 showed show VBD 10_1101-2020_10_26_351783 181 5 that that IN 10_1101-2020_10_26_351783 181 6 Clique Clique NNP 10_1101-2020_10_26_351783 181 7 SuM sum NN 10_1101-2020_10_26_351783 181 8 yielded yield VBD 10_1101-2020_10_26_351783 181 9 the the DT 10_1101-2020_10_26_351783 181 10 far far RB 10_1101-2020_10_26_351783 181 11 highest high JJS 10_1101-2020_10_26_351783 181 12 average average JJ 10_1101-2020_10_26_351783 181 13 enrichment enrichment NN 10_1101-2020_10_26_351783 181 14 score score NN 10_1101-2020_10_26_351783 181 15 ( ( -LRB- 10_1101-2020_10_26_351783 181 16 meta meta NNP 10_1101-2020_10_26_351783 181 17 P P NNP 10_1101-2020_10_26_351783 181 18 = = SYM 10_1101-2020_10_26_351783 181 19 3.2 3.2 CD 10_1101-2020_10_26_351783 181 20 x x SYM 10_1101-2020_10_26_351783 181 21 10 10 CD 10_1101-2020_10_26_351783 181 22 - - SYM 10_1101-2020_10_26_351783 181 23 12 12 CD 10_1101-2020_10_26_351783 181 24 ) ) -RRB- 10_1101-2020_10_26_351783 181 25 and and CC 10_1101-2020_10_26_351783 181 26 was be VBD 10_1101-2020_10_26_351783 181 27 significantly significantly RB 10_1101-2020_10_26_351783 181 28 enriched enrich VBN 10_1101-2020_10_26_351783 181 29 ( ( -LRB- 10_1101-2020_10_26_351783 181 30 P p NN 10_1101-2020_10_26_351783 181 31 < < XX 10_1101-2020_10_26_351783 181 32 0.05 0.05 CD 10_1101-2020_10_26_351783 181 33 ) ) -RRB- 10_1101-2020_10_26_351783 181 34 in in IN 10_1101-2020_10_26_351783 181 35 9/11 9/11 CD 10_1101-2020_10_26_351783 181 36 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 181 37 datasets dataset NNS 10_1101-2020_10_26_351783 181 38 ( ( -LRB- 10_1101-2020_10_26_351783 181 39 Fig fig NN 10_1101-2020_10_26_351783 181 40 . . . 10_1101-2020_10_26_351783 182 1 4a 4a LS 10_1101-2020_10_26_351783 182 2 ) ) -RRB- 10_1101-2020_10_26_351783 182 3 and and CC 10_1101-2020_10_26_351783 182 4 4/9 4/9 CD 10_1101-2020_10_26_351783 182 5 of of IN 10_1101-2020_10_26_351783 182 6 the the DT 10_1101-2020_10_26_351783 182 7 methylation methylation NN 10_1101-2020_10_26_351783 182 8 datasets dataset NNS 10_1101-2020_10_26_351783 182 9 ( ( -LRB- 10_1101-2020_10_26_351783 182 10 Fig fig NN 10_1101-2020_10_26_351783 182 11 . . . 10_1101-2020_10_26_351783 183 1 4b 4b LS 10_1101-2020_10_26_351783 183 2 ) ) -RRB- 10_1101-2020_10_26_351783 183 3 . . . 10_1101-2020_10_26_351783 184 1 From from IN 10_1101-2020_10_26_351783 184 2 the the DT 10_1101-2020_10_26_351783 184 3 significant significant JJ 10_1101-2020_10_26_351783 184 4 modules module NNS 10_1101-2020_10_26_351783 184 5 generated generate VBN 10_1101-2020_10_26_351783 184 6 by by IN 10_1101-2020_10_26_351783 184 7 Clique Clique NNP 10_1101-2020_10_26_351783 184 8 SuM sum NN 10_1101-2020_10_26_351783 184 9 , , , 10_1101-2020_10_26_351783 184 10 we -PRON- PRP 10_1101-2020_10_26_351783 184 11 choose choose VBP 10_1101-2020_10_26_351783 184 12 the the DT 10_1101-2020_10_26_351783 184 13 top top JJ 10_1101-2020_10_26_351783 184 14 four four CD 10_1101-2020_10_26_351783 184 15 modules module NNS 10_1101-2020_10_26_351783 184 16 from from IN 10_1101-2020_10_26_351783 184 17 each each DT 10_1101-2020_10_26_351783 184 18 of of IN 10_1101-2020_10_26_351783 184 19 the the DT 10_1101-2020_10_26_351783 184 20 gene gene NN 10_1101-2020_10_26_351783 184 21 transcription transcription NN 10_1101-2020_10_26_351783 184 22 and and CC 10_1101-2020_10_26_351783 184 23 methylation methylation NN 10_1101-2020_10_26_351783 184 24 sets set NNS 10_1101-2020_10_26_351783 184 25 , , , 10_1101-2020_10_26_351783 184 26 and and CC 10_1101-2020_10_26_351783 184 27 prioritized prioritize VBN 10_1101-2020_10_26_351783 184 28 genes gene NNS 10_1101-2020_10_26_351783 184 29 detected detect VBN 10_1101-2020_10_26_351783 184 30 in in IN 10_1101-2020_10_26_351783 184 31 modules module NNS 10_1101-2020_10_26_351783 184 32 from from IN 10_1101-2020_10_26_351783 184 33 multiple multiple JJ 10_1101-2020_10_26_351783 184 34 datasets dataset NNS 10_1101-2020_10_26_351783 184 35 in in IN 10_1101-2020_10_26_351783 184 36 each each DT 10_1101-2020_10_26_351783 184 37 omic omic JJ 10_1101-2020_10_26_351783 184 38 . . . 10_1101-2020_10_26_351783 185 1 This this DT 10_1101-2020_10_26_351783 185 2 analysis analysis NN 10_1101-2020_10_26_351783 185 3 showed show VBD 10_1101-2020_10_26_351783 185 4 that that IN 10_1101-2020_10_26_351783 185 5 the the DT 10_1101-2020_10_26_351783 185 6 strongest strong JJS 10_1101-2020_10_26_351783 185 7 MS MS NNP 10_1101-2020_10_26_351783 185 8 SNP SNP NNP 10_1101-2020_10_26_351783 185 9 enrichment enrichment NN 10_1101-2020_10_26_351783 185 10 was be VBD 10_1101-2020_10_26_351783 185 11 found find VBN 10_1101-2020_10_26_351783 185 12 for for IN 10_1101-2020_10_26_351783 185 13 genes gene NNS 10_1101-2020_10_26_351783 185 14 in in IN 10_1101-2020_10_26_351783 185 15 at at RB 10_1101-2020_10_26_351783 185 16 least least RBS 10_1101-2020_10_26_351783 185 17 three three CD 10_1101-2020_10_26_351783 185 18 out out IN 10_1101-2020_10_26_351783 185 19 of of IN 10_1101-2020_10_26_351783 185 20 four four CD 10_1101-2020_10_26_351783 185 21 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 185 22 modules module NNS 10_1101-2020_10_26_351783 185 23 ( ( -LRB- 10_1101-2020_10_26_351783 185 24 n=1,552 n=1,552 NNP 10_1101-2020_10_26_351783 185 25 ; ; : 10_1101-2020_10_26_351783 185 26 P= P= NNP 10_1101-2020_10_26_351783 185 27 6.0 6.0 CD 10_1101-2020_10_26_351783 185 28 x x SYM 10_1101-2020_10_26_351783 185 29 10 10 CD 10_1101-2020_10_26_351783 185 30 - - SYM 10_1101-2020_10_26_351783 185 31 7 7 CD 10_1101-2020_10_26_351783 185 32 ) ) -RRB- 10_1101-2020_10_26_351783 185 33 and and CC 10_1101-2020_10_26_351783 185 34 two two CD 10_1101-2020_10_26_351783 185 35 out out IN 10_1101-2020_10_26_351783 185 36 of of IN 10_1101-2020_10_26_351783 185 37 four four CD 10_1101-2020_10_26_351783 185 38 methylomic methylomic JJ 10_1101-2020_10_26_351783 185 39 modules module NNS 10_1101-2020_10_26_351783 185 40 ( ( -LRB- 10_1101-2020_10_26_351783 185 41 n=324 n=324 NNP 10_1101-2020_10_26_351783 185 42 , , , 10_1101-2020_10_26_351783 185 43 P= P= NNP 10_1101-2020_10_26_351783 185 44 1.5x10 1.5x10 CD 10_1101-2020_10_26_351783 185 45 - - SYM 10_1101-2020_10_26_351783 185 46 6 6 CD 10_1101-2020_10_26_351783 185 47 ) ) -RRB- 10_1101-2020_10_26_351783 185 48 . . . 10_1101-2020_10_26_351783 186 1 Next next RB 10_1101-2020_10_26_351783 186 2 , , , 10_1101-2020_10_26_351783 186 3 we -PRON- PRP 10_1101-2020_10_26_351783 186 4 used use VBD 10_1101-2020_10_26_351783 186 5 the the DT 10_1101-2020_10_26_351783 186 6 same same JJ 10_1101-2020_10_26_351783 186 7 principle principle NN 10_1101-2020_10_26_351783 186 8 to to TO 10_1101-2020_10_26_351783 186 9 combine combine VB 10_1101-2020_10_26_351783 186 10 these these DT 10_1101-2020_10_26_351783 186 11 two two CD 10_1101-2020_10_26_351783 186 12 and and CC 10_1101-2020_10_26_351783 186 13 found find VBD 10_1101-2020_10_26_351783 186 14 that that IN 10_1101-2020_10_26_351783 186 15 the the DT 10_1101-2020_10_26_351783 186 16 intersection intersection NN 10_1101-2020_10_26_351783 186 17 between between IN 10_1101-2020_10_26_351783 186 18 the the DT 10_1101-2020_10_26_351783 186 19 gene gene NN 10_1101-2020_10_26_351783 186 20 transcription transcription NN 10_1101-2020_10_26_351783 186 21 and and CC 10_1101-2020_10_26_351783 186 22 methylation methylation NN 10_1101-2020_10_26_351783 186 23 consensus consensus NN 10_1101-2020_10_26_351783 186 24 resulted result VBD 10_1101-2020_10_26_351783 186 25 in in IN 10_1101-2020_10_26_351783 186 26 a a DT 10_1101-2020_10_26_351783 186 27 module module NN 10_1101-2020_10_26_351783 186 28 ( ( -LRB- 10_1101-2020_10_26_351783 186 29 n n NNP 10_1101-2020_10_26_351783 186 30 = = SYM 10_1101-2020_10_26_351783 186 31 220 220 CD 10_1101-2020_10_26_351783 186 32 genes gene NNS 10_1101-2020_10_26_351783 186 33 , , , 10_1101-2020_10_26_351783 186 34 Fig Fig NNP 10_1101-2020_10_26_351783 186 35 . . . 10_1101-2020_10_26_351783 187 1 4 4 LS 10_1101-2020_10_26_351783 187 2 ) ) -RRB- 10_1101-2020_10_26_351783 187 3 enriched enrich VBD 10_1101-2020_10_26_351783 187 4 for for IN 10_1101-2020_10_26_351783 187 5 MS MS NNP 10_1101-2020_10_26_351783 187 6 - - HYPH 10_1101-2020_10_26_351783 187 7 associated associate VBN 10_1101-2020_10_26_351783 187 8 genes gene NNS 10_1101-2020_10_26_351783 187 9 ( ( -LRB- 10_1101-2020_10_26_351783 187 10 75/220 75/220 CD 10_1101-2020_10_26_351783 187 11 , , , 10_1101-2020_10_26_351783 187 12 P p NN 10_1101-2020_10_26_351783 187 13 < < XX 10_1101-2020_10_26_351783 187 14 2.2 2.2 CD 10_1101-2020_10_26_351783 187 15 x x SYM 10_1101-2020_10_26_351783 187 16 10 10 CD 10_1101-2020_10_26_351783 187 17 - - SYM 10_1101-2020_10_26_351783 187 18 16 16 CD 10_1101-2020_10_26_351783 187 19 , , , 10_1101-2020_10_26_351783 187 20 OR or CC 10_1101-2020_10_26_351783 187 21 = = SYM 10_1101-2020_10_26_351783 187 22 7.8 7.8 CD 10_1101-2020_10_26_351783 187 23 ) ) -RRB- 10_1101-2020_10_26_351783 187 24 and and CC 10_1101-2020_10_26_351783 187 25 with with IN 10_1101-2020_10_26_351783 187 26 the the DT 10_1101-2020_10_26_351783 187 27 highest high JJS 10_1101-2020_10_26_351783 187 28 GWAS gwas JJ 10_1101-2020_10_26_351783 187 29 enrichment enrichment NN 10_1101-2020_10_26_351783 187 30 ( ( -LRB- 10_1101-2020_10_26_351783 187 31 P p NN 10_1101-2020_10_26_351783 187 32 = = SYM 10_1101-2020_10_26_351783 187 33 8.8 8.8 CD 10_1101-2020_10_26_351783 187 34 x x SYM 10_1101-2020_10_26_351783 187 35 10 10 CD 10_1101-2020_10_26_351783 187 36 - - SYM 10_1101-2020_10_26_351783 187 37 9 9 CD 10_1101-2020_10_26_351783 187 38 ) ) -RRB- 10_1101-2020_10_26_351783 187 39 which which WDT 10_1101-2020_10_26_351783 187 40 we -PRON- PRP 10_1101-2020_10_26_351783 187 41 hereafter hereafter RB 10_1101-2020_10_26_351783 187 42 referred refer VBD 10_1101-2020_10_26_351783 187 43 to to IN 10_1101-2020_10_26_351783 187 44 as as IN 10_1101-2020_10_26_351783 187 45 the the DT 10_1101-2020_10_26_351783 187 46 multi multi NNS 10_1101-2020_10_26_351783 187 47 - - HYPH 10_1101-2020_10_26_351783 187 48 omics omic NNS 10_1101-2020_10_26_351783 187 49 MS MS NNP 10_1101-2020_10_26_351783 187 50 module module NN 10_1101-2020_10_26_351783 187 51 . . . 10_1101-2020_10_26_351783 188 1 The the DT 10_1101-2020_10_26_351783 188 2 multi multi JJ 10_1101-2020_10_26_351783 188 3 - - HYPH 10_1101-2020_10_26_351783 188 4 omics omic NNS 10_1101-2020_10_26_351783 188 5 MS MS NNP 10_1101-2020_10_26_351783 188 6 module module NN 10_1101-2020_10_26_351783 188 7 was be VBD 10_1101-2020_10_26_351783 188 8 enriched enrich VBN 10_1101-2020_10_26_351783 188 9 in in IN 10_1101-2020_10_26_351783 188 10 genes gene NNS 10_1101-2020_10_26_351783 188 11 associated associate VBN 10_1101-2020_10_26_351783 188 12 with with IN 10_1101-2020_10_26_351783 188 13 major major JJ 10_1101-2020_10_26_351783 188 14 MS MS NNP 10_1101-2020_10_26_351783 188 15 pathways pathway NNS 10_1101-2020_10_26_351783 188 16 . . . 10_1101-2020_10_26_351783 189 1 As as IN 10_1101-2020_10_26_351783 189 2 we -PRON- PRP 10_1101-2020_10_26_351783 189 3 used use VBD 10_1101-2020_10_26_351783 189 4 GWAS GWAS NNP 10_1101-2020_10_26_351783 189 5 enrichment enrichment NN 10_1101-2020_10_26_351783 189 6 as as IN 10_1101-2020_10_26_351783 189 7 a a DT 10_1101-2020_10_26_351783 189 8 selection selection NN 10_1101-2020_10_26_351783 189 9 criterion criterion NN 10_1101-2020_10_26_351783 189 10 , , , 10_1101-2020_10_26_351783 189 11 the the DT 10_1101-2020_10_26_351783 189 12 high high JJ 10_1101-2020_10_26_351783 189 13 GWAS GWAS NNP 10_1101-2020_10_26_351783 189 14 enrichment enrichment NN 10_1101-2020_10_26_351783 189 15 of of IN 10_1101-2020_10_26_351783 189 16 the the DT 10_1101-2020_10_26_351783 189 17 final final JJ 10_1101-2020_10_26_351783 189 18 module module NN 10_1101-2020_10_26_351783 189 19 was be VBD 10_1101-2020_10_26_351783 189 20 partly partly RB 10_1101-2020_10_26_351783 189 21 expected expect VBN 10_1101-2020_10_26_351783 189 22 , , , 10_1101-2020_10_26_351783 189 23 which which WDT 10_1101-2020_10_26_351783 189 24 led lead VBD 10_1101-2020_10_26_351783 189 25 us -PRON- PRP 10_1101-2020_10_26_351783 189 26 to to TO 10_1101-2020_10_26_351783 189 27 analyze analyze VB 10_1101-2020_10_26_351783 189 28 its -PRON- PRP$ 10_1101-2020_10_26_351783 189 29 biological biological JJ 10_1101-2020_10_26_351783 189 30 functions function NNS 10_1101-2020_10_26_351783 189 31 and and CC 10_1101-2020_10_26_351783 189 32 their -PRON- PRP$ 10_1101-2020_10_26_351783 189 33 potential potential JJ 10_1101-2020_10_26_351783 189 34 epigenetic epigenetic JJ 10_1101-2020_10_26_351783 189 35 associations association NNS 10_1101-2020_10_26_351783 189 36 to to IN 10_1101-2020_10_26_351783 189 37 MS MS NNP 10_1101-2020_10_26_351783 189 38 . . . 10_1101-2020_10_26_351783 189 39 First first RB 10_1101-2020_10_26_351783 189 40 , , , 10_1101-2020_10_26_351783 189 41 pathway pathway JJ 10_1101-2020_10_26_351783 189 42 enrichment enrichment NN 10_1101-2020_10_26_351783 189 43 analysis analysis NN 10_1101-2020_10_26_351783 189 44 showed show VBD 10_1101-2020_10_26_351783 189 45 that that IN 10_1101-2020_10_26_351783 189 46 the the DT 10_1101-2020_10_26_351783 189 47 multi multi JJ 10_1101-2020_10_26_351783 189 48 - - JJ 10_1101-2020_10_26_351783 189 49 omics omics JJ 10_1101-2020_10_26_351783 189 50 module module NNP 10_1101-2020_10_26_351783 189 51 genes gene NNS 10_1101-2020_10_26_351783 189 52 ( ( -LRB- 10_1101-2020_10_26_351783 189 53 which which WDT 10_1101-2020_10_26_351783 189 54 was be VBD 10_1101-2020_10_26_351783 189 55 not not RB 10_1101-2020_10_26_351783 189 56 certified certify VBN 10_1101-2020_10_26_351783 189 57 by by IN 10_1101-2020_10_26_351783 189 58 peer peer NN 10_1101-2020_10_26_351783 189 59 review review NN 10_1101-2020_10_26_351783 189 60 ) ) -RRB- 10_1101-2020_10_26_351783 189 61 is be VBZ 10_1101-2020_10_26_351783 189 62 the the DT 10_1101-2020_10_26_351783 189 63 author author NN 10_1101-2020_10_26_351783 189 64 / / SYM 10_1101-2020_10_26_351783 189 65 funder funder NN 10_1101-2020_10_26_351783 189 66 . . . 10_1101-2020_10_26_351783 190 1 All all DT 10_1101-2020_10_26_351783 190 2 rights right NNS 10_1101-2020_10_26_351783 190 3 reserved reserve VBD 10_1101-2020_10_26_351783 190 4 . . . 10_1101-2020_10_26_351783 191 1 No no DT 10_1101-2020_10_26_351783 191 2 reuse reuse NN 10_1101-2020_10_26_351783 191 3 allowed allow VBN 10_1101-2020_10_26_351783 191 4 without without IN 10_1101-2020_10_26_351783 191 5 permission permission NN 10_1101-2020_10_26_351783 191 6 . . . 10_1101-2020_10_26_351783 192 1 The the DT 10_1101-2020_10_26_351783 192 2 copyright copyright NN 10_1101-2020_10_26_351783 192 3 holder holder NN 10_1101-2020_10_26_351783 192 4 for for IN 10_1101-2020_10_26_351783 192 5 this this DT 10_1101-2020_10_26_351783 192 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 192 7 version version NN 10_1101-2020_10_26_351783 192 8 posted post VBD 10_1101-2020_10_26_351783 192 9 January January NNP 10_1101-2020_10_26_351783 192 10 6 6 CD 10_1101-2020_10_26_351783 192 11 , , , 10_1101-2020_10_26_351783 192 12 2021 2021 CD 10_1101-2020_10_26_351783 192 13 . . . 10_1101-2020_10_26_351783 192 14 ; ; : 10_1101-2020_10_26_351783 192 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 192 16 : : : 10_1101-2020_10_26_351783 192 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 192 18 preprint preprint NN 10_1101-2020_10_26_351783 192 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 192 20 13 13 CD 10_1101-2020_10_26_351783 192 21 are be VBP 10_1101-2020_10_26_351783 192 22 significantly significantly RB 10_1101-2020_10_26_351783 192 23 involved involve VBN 10_1101-2020_10_26_351783 192 24 in in IN 10_1101-2020_10_26_351783 192 25 several several JJ 10_1101-2020_10_26_351783 192 26 inter inter NN 10_1101-2020_10_26_351783 192 27 - - JJ 10_1101-2020_10_26_351783 192 28 linked link VBN 10_1101-2020_10_26_351783 192 29 immune immune NN 10_1101-2020_10_26_351783 192 30 - - HYPH 10_1101-2020_10_26_351783 192 31 related relate VBN 10_1101-2020_10_26_351783 192 32 pathways pathway NNS 10_1101-2020_10_26_351783 192 33 , , , 10_1101-2020_10_26_351783 192 34 most most JJS 10_1101-2020_10_26_351783 192 35 of of IN 10_1101-2020_10_26_351783 192 36 which which WDT 10_1101-2020_10_26_351783 192 37 have have VBP 10_1101-2020_10_26_351783 192 38 been be VBN 10_1101-2020_10_26_351783 192 39 previously previously RB 10_1101-2020_10_26_351783 192 40 associated associate VBN 10_1101-2020_10_26_351783 192 41 to to IN 10_1101-2020_10_26_351783 192 42 MS MS NNP 10_1101-2020_10_26_351783 192 43 , , , 10_1101-2020_10_26_351783 192 44 including include VBG 10_1101-2020_10_26_351783 192 45 the the DT 10_1101-2020_10_26_351783 192 46 T T NNP 10_1101-2020_10_26_351783 192 47 cell cell NN 10_1101-2020_10_26_351783 192 48 receptor[25 receptor[25 NNP 10_1101-2020_10_26_351783 192 49 ] ] -RRB- 10_1101-2020_10_26_351783 192 50 ( ( -LRB- 10_1101-2020_10_26_351783 192 51 adjusted adjust VBN 10_1101-2020_10_26_351783 192 52 P p NN 10_1101-2020_10_26_351783 192 53 = = SYM 10_1101-2020_10_26_351783 192 54 3.6 3.6 CD 10_1101-2020_10_26_351783 192 55 x x SYM 10_1101-2020_10_26_351783 192 56 10 10 CD 10_1101-2020_10_26_351783 192 57 - - SYM 10_1101-2020_10_26_351783 192 58 47 47 CD 10_1101-2020_10_26_351783 192 59 ) ) -RRB- 10_1101-2020_10_26_351783 192 60 , , , 10_1101-2020_10_26_351783 192 61 PI3K PI3K NNP 10_1101-2020_10_26_351783 192 62 / / SYM 10_1101-2020_10_26_351783 192 63 Akt[26 Akt[26 NFP 10_1101-2020_10_26_351783 192 64 ] ] -RRB- 10_1101-2020_10_26_351783 192 65 ( ( -LRB- 10_1101-2020_10_26_351783 192 66 P p NN 10_1101-2020_10_26_351783 192 67 = = SYM 10_1101-2020_10_26_351783 192 68 4.6 4.6 CD 10_1101-2020_10_26_351783 192 69 x x SYM 10_1101-2020_10_26_351783 192 70 10 10 CD 10_1101-2020_10_26_351783 192 71 - - SYM 10_1101-2020_10_26_351783 192 72 35 35 CD 10_1101-2020_10_26_351783 192 73 ) ) -RRB- 10_1101-2020_10_26_351783 192 74 , , , 10_1101-2020_10_26_351783 192 75 ErbB[27 ErbB[27 VBN 10_1101-2020_10_26_351783 192 76 ] ] -RRB- 10_1101-2020_10_26_351783 192 77 ( ( -LRB- 10_1101-2020_10_26_351783 192 78 P p NN 10_1101-2020_10_26_351783 192 79 = = SYM 10_1101-2020_10_26_351783 192 80 7.7 7.7 CD 10_1101-2020_10_26_351783 192 81 x x SYM 10_1101-2020_10_26_351783 192 82 10 10 CD 10_1101-2020_10_26_351783 192 83 - - SYM 10_1101-2020_10_26_351783 192 84 32 32 CD 10_1101-2020_10_26_351783 192 85 ) ) -RRB- 10_1101-2020_10_26_351783 192 86 , , , 10_1101-2020_10_26_351783 192 87 Fc Fc NNP 10_1101-2020_10_26_351783 192 88 epsilon epsilon NN 10_1101-2020_10_26_351783 192 89 RI[28 RI[28 NNS 10_1101-2020_10_26_351783 192 90 ] ] -RRB- 10_1101-2020_10_26_351783 192 91 ( ( -LRB- 10_1101-2020_10_26_351783 192 92 P p NN 10_1101-2020_10_26_351783 192 93 = = SYM 10_1101-2020_10_26_351783 192 94 8.3 8.3 CD 10_1101-2020_10_26_351783 192 95 x x SYM 10_1101-2020_10_26_351783 192 96 10 10 CD 10_1101-2020_10_26_351783 192 97 - - SYM 10_1101-2020_10_26_351783 192 98 30 30 CD 10_1101-2020_10_26_351783 192 99 ) ) -RRB- 10_1101-2020_10_26_351783 192 100 , , , 10_1101-2020_10_26_351783 192 101 chemokine[29,30 chemokine[29,30 CD 10_1101-2020_10_26_351783 192 102 ] ] -RRB- 10_1101-2020_10_26_351783 192 103 ( ( -LRB- 10_1101-2020_10_26_351783 192 104 P p NN 10_1101-2020_10_26_351783 192 105 = = SYM 10_1101-2020_10_26_351783 192 106 2.6 2.6 CD 10_1101-2020_10_26_351783 192 107 x x SYM 10_1101-2020_10_26_351783 192 108 10 10 CD 10_1101-2020_10_26_351783 192 109 - - SYM 10_1101-2020_10_26_351783 192 110 28 28 CD 10_1101-2020_10_26_351783 192 111 ) ) -RRB- 10_1101-2020_10_26_351783 192 112 , , , 10_1101-2020_10_26_351783 192 113 MAPK[31,32 mapk[31,32 NN 10_1101-2020_10_26_351783 192 114 ] ] -RRB- 10_1101-2020_10_26_351783 192 115 ( ( -LRB- 10_1101-2020_10_26_351783 192 116 P p NN 10_1101-2020_10_26_351783 192 117 = = SYM 10_1101-2020_10_26_351783 192 118 2.0 2.0 CD 10_1101-2020_10_26_351783 192 119 x x SYM 10_1101-2020_10_26_351783 192 120 10 10 CD 10_1101-2020_10_26_351783 192 121 - - SYM 10_1101-2020_10_26_351783 192 122 25 25 CD 10_1101-2020_10_26_351783 192 123 ) ) -RRB- 10_1101-2020_10_26_351783 192 124 , , , 10_1101-2020_10_26_351783 192 125 and and CC 10_1101-2020_10_26_351783 192 126 B b NN 10_1101-2020_10_26_351783 192 127 cell cell NN 10_1101-2020_10_26_351783 192 128 receptor[32 receptor[32 NNP 10_1101-2020_10_26_351783 192 129 ] ] -RRB- 10_1101-2020_10_26_351783 192 130 ( ( -LRB- 10_1101-2020_10_26_351783 192 131 P p NN 10_1101-2020_10_26_351783 192 132 = = SYM 10_1101-2020_10_26_351783 192 133 3.9 3.9 CD 10_1101-2020_10_26_351783 192 134 x x SYM 10_1101-2020_10_26_351783 192 135 10 10 CD 10_1101-2020_10_26_351783 192 136 - - SYM 10_1101-2020_10_26_351783 192 137 19 19 CD 10_1101-2020_10_26_351783 192 138 ) ) -RRB- 10_1101-2020_10_26_351783 192 139 signaling signal VBG 10_1101-2020_10_26_351783 192 140 pathways pathway NNS 10_1101-2020_10_26_351783 192 141 ; ; , 10_1101-2020_10_26_351783 192 142 Th17 Th17 NNP 10_1101-2020_10_26_351783 192 143 ( ( -LRB- 10_1101-2020_10_26_351783 192 144 P p NN 10_1101-2020_10_26_351783 192 145 = = SYM 10_1101-2020_10_26_351783 192 146 9.6 9.6 CD 10_1101-2020_10_26_351783 192 147 x x SYM 10_1101-2020_10_26_351783 192 148 10 10 CD 10_1101-2020_10_26_351783 192 149 - - SYM 10_1101-2020_10_26_351783 192 150 29 29 CD 10_1101-2020_10_26_351783 192 151 ) ) -RRB- 10_1101-2020_10_26_351783 192 152 , , , 10_1101-2020_10_26_351783 192 153 and and CC 10_1101-2020_10_26_351783 192 154 Th1 th1 NN 10_1101-2020_10_26_351783 192 155 and and CC 10_1101-2020_10_26_351783 192 156 Th2 th2 NN 10_1101-2020_10_26_351783 192 157 ( ( -LRB- 10_1101-2020_10_26_351783 192 158 P p NN 10_1101-2020_10_26_351783 192 159 = = SYM 10_1101-2020_10_26_351783 192 160 6.9 6.9 CD 10_1101-2020_10_26_351783 192 161 x x SYM 10_1101-2020_10_26_351783 192 162 10 10 CD 10_1101-2020_10_26_351783 192 163 - - SYM 10_1101-2020_10_26_351783 192 164 19 19 CD 10_1101-2020_10_26_351783 192 165 ) ) -RRB- 10_1101-2020_10_26_351783 192 166 cell cell NN 10_1101-2020_10_26_351783 192 167 differentiation[33 differentiation[33 NN 10_1101-2020_10_26_351783 192 168 ] ] -RRB- 10_1101-2020_10_26_351783 192 169 ; ; , 10_1101-2020_10_26_351783 192 170 natural natural JJ 10_1101-2020_10_26_351783 192 171 killer killer NN 10_1101-2020_10_26_351783 192 172 cell cell NN 10_1101-2020_10_26_351783 192 173 mediated mediate VBD 10_1101-2020_10_26_351783 192 174 cytotoxicity cytotoxicity NN 10_1101-2020_10_26_351783 192 175 ( ( -LRB- 10_1101-2020_10_26_351783 192 176 P p NN 10_1101-2020_10_26_351783 192 177 = = SYM 10_1101-2020_10_26_351783 192 178 1.6 1.6 CD 10_1101-2020_10_26_351783 192 179 x x SYM 10_1101-2020_10_26_351783 192 180 10 10 CD 10_1101-2020_10_26_351783 192 181 - - SYM 10_1101-2020_10_26_351783 192 182 27 27 CD 10_1101-2020_10_26_351783 192 183 ) ) -RRB- 10_1101-2020_10_26_351783 192 184 ; ; : 10_1101-2020_10_26_351783 192 185 and and CC 10_1101-2020_10_26_351783 192 186 leukocyte leukocyte NN 10_1101-2020_10_26_351783 192 187 transendothelial transendothelial NN 10_1101-2020_10_26_351783 192 188 migration migration NN 10_1101-2020_10_26_351783 192 189 ( ( -LRB- 10_1101-2020_10_26_351783 192 190 P p NN 10_1101-2020_10_26_351783 192 191 = = SYM 10_1101-2020_10_26_351783 192 192 3.9 3.9 CD 10_1101-2020_10_26_351783 192 193 x x SYM 10_1101-2020_10_26_351783 192 194 10 10 CD 10_1101-2020_10_26_351783 192 195 - - SYM 10_1101-2020_10_26_351783 192 196 20 20 CD 10_1101-2020_10_26_351783 192 197 ) ) -RRB- 10_1101-2020_10_26_351783 192 198 , , , 10_1101-2020_10_26_351783 192 199 which which WDT 10_1101-2020_10_26_351783 192 200 indeed indeed RB 10_1101-2020_10_26_351783 192 201 supports support VBZ 10_1101-2020_10_26_351783 192 202 their -PRON- PRP$ 10_1101-2020_10_26_351783 192 203 relevance relevance NN 10_1101-2020_10_26_351783 192 204 in in IN 10_1101-2020_10_26_351783 192 205 MS MS NNP 10_1101-2020_10_26_351783 192 206 . . . 10_1101-2020_10_26_351783 192 207 Interestingly interestingly RB 10_1101-2020_10_26_351783 192 208 , , , 10_1101-2020_10_26_351783 192 209 the the DT 10_1101-2020_10_26_351783 192 210 module module NN 10_1101-2020_10_26_351783 192 211 was be VBD 10_1101-2020_10_26_351783 192 212 also also RB 10_1101-2020_10_26_351783 192 213 highly highly RB 10_1101-2020_10_26_351783 192 214 enriched enrich VBN 10_1101-2020_10_26_351783 192 215 in in IN 10_1101-2020_10_26_351783 192 216 morphogenetic morphogenetic JJ 10_1101-2020_10_26_351783 192 217 and and CC 10_1101-2020_10_26_351783 192 218 neurogenetic neurogenetic JJ 10_1101-2020_10_26_351783 192 219 signaling signaling NN 10_1101-2020_10_26_351783 192 220 pathways pathway NNS 10_1101-2020_10_26_351783 192 221 , , , 10_1101-2020_10_26_351783 192 222 such such JJ 10_1101-2020_10_26_351783 192 223 as as IN 10_1101-2020_10_26_351783 192 224 the the DT 10_1101-2020_10_26_351783 192 225 neurotrophin neurotrophin NN 10_1101-2020_10_26_351783 192 226 ( ( -LRB- 10_1101-2020_10_26_351783 192 227 adjusted adjust VBN 10_1101-2020_10_26_351783 192 228 P p NN 10_1101-2020_10_26_351783 192 229 = = SYM 10_1101-2020_10_26_351783 192 230 1.3 1.3 CD 10_1101-2020_10_26_351783 192 231 x x SYM 10_1101-2020_10_26_351783 192 232 10 10 CD 10_1101-2020_10_26_351783 192 233 - - SYM 10_1101-2020_10_26_351783 192 234 36 36 CD 10_1101-2020_10_26_351783 192 235 ) ) -RRB- 10_1101-2020_10_26_351783 192 236 , , , 10_1101-2020_10_26_351783 192 237 Ras Ras NNP 10_1101-2020_10_26_351783 192 238 ( ( -LRB- 10_1101-2020_10_26_351783 192 239 P p NN 10_1101-2020_10_26_351783 192 240 = = SYM 10_1101-2020_10_26_351783 192 241 1.4 1.4 CD 10_1101-2020_10_26_351783 192 242 x x SYM 10_1101-2020_10_26_351783 192 243 10 10 CD 10_1101-2020_10_26_351783 192 244 - - SYM 10_1101-2020_10_26_351783 192 245 36 36 CD 10_1101-2020_10_26_351783 192 246 ) ) -RRB- 10_1101-2020_10_26_351783 192 247 , , , 10_1101-2020_10_26_351783 192 248 Rap1 Rap1 NNP 10_1101-2020_10_26_351783 192 249 ( ( -LRB- 10_1101-2020_10_26_351783 192 250 P p NN 10_1101-2020_10_26_351783 192 251 = = SYM 10_1101-2020_10_26_351783 192 252 2.2 2.2 CD 10_1101-2020_10_26_351783 192 253 x x SYM 10_1101-2020_10_26_351783 192 254 10 10 CD 10_1101-2020_10_26_351783 192 255 - - SYM 10_1101-2020_10_26_351783 192 256 35 35 CD 10_1101-2020_10_26_351783 192 257 ) ) -RRB- 10_1101-2020_10_26_351783 192 258 , , , 10_1101-2020_10_26_351783 192 259 vascular vascular JJ 10_1101-2020_10_26_351783 192 260 endothelial endothelial JJ 10_1101-2020_10_26_351783 192 261 growth growth NN 10_1101-2020_10_26_351783 192 262 factor factor NN 10_1101-2020_10_26_351783 192 263 ( ( -LRB- 10_1101-2020_10_26_351783 192 264 VEGF vegf NN 10_1101-2020_10_26_351783 192 265 , , , 10_1101-2020_10_26_351783 192 266 P p NN 10_1101-2020_10_26_351783 192 267 = = SYM 10_1101-2020_10_26_351783 192 268 1.7 1.7 CD 10_1101-2020_10_26_351783 192 269 x x SYM 10_1101-2020_10_26_351783 192 270 10 10 CD 10_1101-2020_10_26_351783 192 271 - - SYM 10_1101-2020_10_26_351783 192 272 27 27 CD 10_1101-2020_10_26_351783 192 273 ) ) -RRB- 10_1101-2020_10_26_351783 192 274 , , , 10_1101-2020_10_26_351783 192 275 FoxO FoxO NNP 10_1101-2020_10_26_351783 192 276 ( ( -LRB- 10_1101-2020_10_26_351783 192 277 P p NN 10_1101-2020_10_26_351783 192 278 = = SYM 10_1101-2020_10_26_351783 192 279 3.6 3.6 CD 10_1101-2020_10_26_351783 192 280 x x SYM 10_1101-2020_10_26_351783 192 281 10 10 CD 10_1101-2020_10_26_351783 192 282 - - SYM 10_1101-2020_10_26_351783 192 283 27 27 CD 10_1101-2020_10_26_351783 192 284 ) ) -RRB- 10_1101-2020_10_26_351783 192 285 , , , 10_1101-2020_10_26_351783 192 286 and and CC 10_1101-2020_10_26_351783 192 287 mTOR mTOR NNS 10_1101-2020_10_26_351783 192 288 ( ( -LRB- 10_1101-2020_10_26_351783 192 289 P p NN 10_1101-2020_10_26_351783 192 290 = = SYM 10_1101-2020_10_26_351783 192 291 4.1 4.1 CD 10_1101-2020_10_26_351783 192 292 x x SYM 10_1101-2020_10_26_351783 192 293 10 10 CD 10_1101-2020_10_26_351783 192 294 - - SYM 10_1101-2020_10_26_351783 192 295 14 14 CD 10_1101-2020_10_26_351783 192 296 ) ) -RRB- 10_1101-2020_10_26_351783 192 297 signaling signal VBG 10_1101-2020_10_26_351783 192 298 pathways pathway NNS 10_1101-2020_10_26_351783 192 299 ; ; , 10_1101-2020_10_26_351783 192 300 and and CC 10_1101-2020_10_26_351783 192 301 in in IN 10_1101-2020_10_26_351783 192 302 growth growth NN 10_1101-2020_10_26_351783 192 303 hormone hormone NN 10_1101-2020_10_26_351783 192 304 synthesis synthesis NN 10_1101-2020_10_26_351783 192 305 , , , 10_1101-2020_10_26_351783 192 306 secretion secretion NN 10_1101-2020_10_26_351783 192 307 and and CC 10_1101-2020_10_26_351783 192 308 action action NN 10_1101-2020_10_26_351783 192 309 ( ( -LRB- 10_1101-2020_10_26_351783 192 310 P p NN 10_1101-2020_10_26_351783 192 311 = = SYM 10_1101-2020_10_26_351783 192 312 6.6 6.6 CD 10_1101-2020_10_26_351783 192 313 x x SYM 10_1101-2020_10_26_351783 192 314 10 10 CD 10_1101-2020_10_26_351783 192 315 - - SYM 10_1101-2020_10_26_351783 192 316 31 31 CD 10_1101-2020_10_26_351783 192 317 ) ) -RRB- 10_1101-2020_10_26_351783 192 318 . . . 10_1101-2020_10_26_351783 193 1 The the DT 10_1101-2020_10_26_351783 193 2 multi multi JJ 10_1101-2020_10_26_351783 193 3 - - HYPH 10_1101-2020_10_26_351783 193 4 omics omic NNS 10_1101-2020_10_26_351783 193 5 MS MS NNP 10_1101-2020_10_26_351783 193 6 module module NN 10_1101-2020_10_26_351783 193 7 was be VBD 10_1101-2020_10_26_351783 193 8 enriched enrich VBN 10_1101-2020_10_26_351783 193 9 in in IN 10_1101-2020_10_26_351783 193 10 genes gene NNS 10_1101-2020_10_26_351783 193 11 associated associate VBN 10_1101-2020_10_26_351783 193 12 with with IN 10_1101-2020_10_26_351783 193 13 five five CD 10_1101-2020_10_26_351783 193 14 known know VBN 10_1101-2020_10_26_351783 193 15 environmental environmental JJ 10_1101-2020_10_26_351783 193 16 MS MS NNP 10_1101-2020_10_26_351783 193 17 risk risk NN 10_1101-2020_10_26_351783 193 18 factors factor NNS 10_1101-2020_10_26_351783 193 19 validated validate VBN 10_1101-2020_10_26_351783 193 20 in in IN 10_1101-2020_10_26_351783 193 21 an an DT 10_1101-2020_10_26_351783 193 22 independent independent JJ 10_1101-2020_10_26_351783 193 23 cohort cohort NN 10_1101-2020_10_26_351783 193 24 . . . 10_1101-2020_10_26_351783 194 1 Second second JJ 10_1101-2020_10_26_351783 194 2 , , , 10_1101-2020_10_26_351783 194 3 from from IN 10_1101-2020_10_26_351783 194 4 a a DT 10_1101-2020_10_26_351783 194 5 literature literature NN 10_1101-2020_10_26_351783 194 6 study[34,35 study[34,35 NNS 10_1101-2020_10_26_351783 194 7 ] ] -RRB- 10_1101-2020_10_26_351783 194 8 we -PRON- PRP 10_1101-2020_10_26_351783 194 9 found find VBD 10_1101-2020_10_26_351783 194 10 nine nine CD 10_1101-2020_10_26_351783 194 11 environmental environmental JJ 10_1101-2020_10_26_351783 194 12 MS MS NNP 10_1101-2020_10_26_351783 194 13 risk risk NN 10_1101-2020_10_26_351783 194 14 factors factor NNS 10_1101-2020_10_26_351783 194 15 of of IN 10_1101-2020_10_26_351783 194 16 varying vary VBG 10_1101-2020_10_26_351783 194 17 evidence evidence NN 10_1101-2020_10_26_351783 194 18 for for IN 10_1101-2020_10_26_351783 194 19 which which WDT 10_1101-2020_10_26_351783 194 20 we -PRON- PRP 10_1101-2020_10_26_351783 194 21 could could MD 10_1101-2020_10_26_351783 194 22 identify identify VB 10_1101-2020_10_26_351783 194 23 methylation methylation NN 10_1101-2020_10_26_351783 194 24 studies study NNS 10_1101-2020_10_26_351783 194 25 in in IN 10_1101-2020_10_26_351783 194 26 healthy healthy JJ 10_1101-2020_10_26_351783 194 27 controls control NNS 10_1101-2020_10_26_351783 194 28 . . . 10_1101-2020_10_26_351783 195 1 For for IN 10_1101-2020_10_26_351783 195 2 each each DT 10_1101-2020_10_26_351783 195 3 of of IN 10_1101-2020_10_26_351783 195 4 these these DT 10_1101-2020_10_26_351783 195 5 risk risk NN 10_1101-2020_10_26_351783 195 6 factors factor NNS 10_1101-2020_10_26_351783 195 7 we -PRON- PRP 10_1101-2020_10_26_351783 195 8 derived derive VBD 10_1101-2020_10_26_351783 195 9 the the DT 10_1101-2020_10_26_351783 195 10 top top JJ 10_1101-2020_10_26_351783 195 11 1000 1000 CD 10_1101-2020_10_26_351783 195 12 differentially differentially RB 10_1101-2020_10_26_351783 195 13 methylated methylate VBN 10_1101-2020_10_26_351783 195 14 genes gene NNS 10_1101-2020_10_26_351783 195 15 ( ( -LRB- 10_1101-2020_10_26_351783 195 16 DMGs DMGs NNP 10_1101-2020_10_26_351783 195 17 ) ) -RRB- 10_1101-2020_10_26_351783 195 18 and and CC 10_1101-2020_10_26_351783 195 19 tested test VBD 10_1101-2020_10_26_351783 195 20 their -PRON- PRP$ 10_1101-2020_10_26_351783 195 21 enrichment enrichment NN 10_1101-2020_10_26_351783 195 22 with with IN 10_1101-2020_10_26_351783 195 23 the the DT 10_1101-2020_10_26_351783 195 24 module module NN 10_1101-2020_10_26_351783 195 25 . . . 10_1101-2020_10_26_351783 196 1 Intriguingly intriguingly RB 10_1101-2020_10_26_351783 196 2 , , , 10_1101-2020_10_26_351783 196 3 the the DT 10_1101-2020_10_26_351783 196 4 module module NN 10_1101-2020_10_26_351783 196 5 was be VBD 10_1101-2020_10_26_351783 196 6 significantly significantly RB 10_1101-2020_10_26_351783 196 7 enriched enrich VBN 10_1101-2020_10_26_351783 196 8 for for IN 10_1101-2020_10_26_351783 196 9 genes gene NNS 10_1101-2020_10_26_351783 196 10 associated associate VBN 10_1101-2020_10_26_351783 196 11 with with IN 10_1101-2020_10_26_351783 196 12 five five CD 10_1101-2020_10_26_351783 196 13 risk risk NN 10_1101-2020_10_26_351783 196 14 factors factor NNS 10_1101-2020_10_26_351783 196 15 ( ( -LRB- 10_1101-2020_10_26_351783 196 16 Fig fig NN 10_1101-2020_10_26_351783 196 17 . . . 10_1101-2020_10_26_351783 197 1 5b 5b NN 10_1101-2020_10_26_351783 197 2 ) ) -RRB- 10_1101-2020_10_26_351783 197 3 , , , 10_1101-2020_10_26_351783 197 4 which which WDT 10_1101-2020_10_26_351783 197 5 included include VBD 10_1101-2020_10_26_351783 197 6 the the DT 10_1101-2020_10_26_351783 197 7 top top JJ 10_1101-2020_10_26_351783 197 8 associated associate VBN 10_1101-2020_10_26_351783 197 9 risk risk NN 10_1101-2020_10_26_351783 197 10 factors factor NNS 10_1101-2020_10_26_351783 197 11 , , , 10_1101-2020_10_26_351783 197 12 i.e. i.e. FW 10_1101-2020_10_26_351783 197 13 , , , 10_1101-2020_10_26_351783 197 14 Epstein Epstein NNP 10_1101-2020_10_26_351783 197 15 - - HYPH 10_1101-2020_10_26_351783 197 16 Barr Barr NNP 10_1101-2020_10_26_351783 197 17 virus virus NN 10_1101-2020_10_26_351783 197 18 ( ( -LRB- 10_1101-2020_10_26_351783 197 19 EBV EBV NNP 10_1101-2020_10_26_351783 197 20 ) ) -RRB- 10_1101-2020_10_26_351783 197 21 infection infection NN 10_1101-2020_10_26_351783 197 22 ( ( -LRB- 10_1101-2020_10_26_351783 197 23 Fisher Fisher NNP 10_1101-2020_10_26_351783 197 24 exact exact JJ 10_1101-2020_10_26_351783 197 25 test test NN 10_1101-2020_10_26_351783 197 26 P p NN 10_1101-2020_10_26_351783 197 27 = = SYM 10_1101-2020_10_26_351783 197 28 1.5 1.5 CD 10_1101-2020_10_26_351783 197 29 x x SYM 10_1101-2020_10_26_351783 197 30 10 10 CD 10_1101-2020_10_26_351783 197 31 - - SYM 10_1101-2020_10_26_351783 197 32 3 3 CD 10_1101-2020_10_26_351783 197 33 , , , 10_1101-2020_10_26_351783 197 34 OR or CC 10_1101-2020_10_26_351783 197 35 = = SYM 10_1101-2020_10_26_351783 197 36 2.1 2.1 CD 10_1101-2020_10_26_351783 197 37 ) ) -RRB- 10_1101-2020_10_26_351783 197 38 and and CC 10_1101-2020_10_26_351783 197 39 smoking smoking NN 10_1101-2020_10_26_351783 197 40 ( ( -LRB- 10_1101-2020_10_26_351783 197 41 P p NN 10_1101-2020_10_26_351783 197 42 = = SYM 10_1101-2020_10_26_351783 197 43 1.2 1.2 CD 10_1101-2020_10_26_351783 197 44 x x SYM 10_1101-2020_10_26_351783 197 45 10 10 CD 10_1101-2020_10_26_351783 197 46 - - SYM 10_1101-2020_10_26_351783 197 47 4 4 CD 10_1101-2020_10_26_351783 197 48 , , , 10_1101-2020_10_26_351783 197 49 OR or CC 10_1101-2020_10_26_351783 197 50 = = SYM 10_1101-2020_10_26_351783 197 51 2.3 2.3 CD 10_1101-2020_10_26_351783 197 52 ) ) -RRB- 10_1101-2020_10_26_351783 197 53 , , , 10_1101-2020_10_26_351783 197 54 as as RB 10_1101-2020_10_26_351783 197 55 well well RB 10_1101-2020_10_26_351783 197 56 as as IN 10_1101-2020_10_26_351783 197 57 low low JJ 10_1101-2020_10_26_351783 197 58 sun sun NN 10_1101-2020_10_26_351783 197 59 exposure exposure NN 10_1101-2020_10_26_351783 197 60 ( ( -LRB- 10_1101-2020_10_26_351783 197 61 P p NN 10_1101-2020_10_26_351783 197 62 = = SYM 10_1101-2020_10_26_351783 197 63 1.2 1.2 CD 10_1101-2020_10_26_351783 197 64 x x SYM 10_1101-2020_10_26_351783 197 65 10 10 CD 10_1101-2020_10_26_351783 197 66 - - SYM 10_1101-2020_10_26_351783 197 67 4 4 CD 10_1101-2020_10_26_351783 197 68 , , , 10_1101-2020_10_26_351783 197 69 OR or CC 10_1101-2020_10_26_351783 197 70 = = SYM 10_1101-2020_10_26_351783 197 71 2.3 2.3 CD 10_1101-2020_10_26_351783 197 72 ) ) -RRB- 10_1101-2020_10_26_351783 197 73 , , , 10_1101-2020_10_26_351783 197 74 high high JJ 10_1101-2020_10_26_351783 197 75 BMI BMI NNP 10_1101-2020_10_26_351783 197 76 ( ( -LRB- 10_1101-2020_10_26_351783 197 77 P p NN 10_1101-2020_10_26_351783 197 78 = = SYM 10_1101-2020_10_26_351783 197 79 0.023 0.023 CD 10_1101-2020_10_26_351783 197 80 , , , 10_1101-2020_10_26_351783 197 81 OR or CC 10_1101-2020_10_26_351783 197 82 = = SYM 10_1101-2020_10_26_351783 197 83 1.7 1.7 CD 10_1101-2020_10_26_351783 197 84 ) ) -RRB- 10_1101-2020_10_26_351783 197 85 and and CC 10_1101-2020_10_26_351783 197 86 alcohol alcohol NN 10_1101-2020_10_26_351783 197 87 consumption consumption NN 10_1101-2020_10_26_351783 197 88 ( ( -LRB- 10_1101-2020_10_26_351783 197 89 P p NN 10_1101-2020_10_26_351783 197 90 = = SYM 10_1101-2020_10_26_351783 197 91 2.9 2.9 CD 10_1101-2020_10_26_351783 197 92 x x SYM 10_1101-2020_10_26_351783 197 93 10 10 CD 10_1101-2020_10_26_351783 197 94 - - SYM 10_1101-2020_10_26_351783 197 95 4 4 CD 10_1101-2020_10_26_351783 197 96 , , , 10_1101-2020_10_26_351783 197 97 OR or CC 10_1101-2020_10_26_351783 197 98 = = SYM 10_1101-2020_10_26_351783 197 99 2.2 2.2 CD 10_1101-2020_10_26_351783 197 100 ) ) -RRB- 10_1101-2020_10_26_351783 197 101 . . . 10_1101-2020_10_26_351783 198 1 Then then RB 10_1101-2020_10_26_351783 198 2 , , , 10_1101-2020_10_26_351783 198 3 we -PRON- PRP 10_1101-2020_10_26_351783 198 4 asked ask VBD 10_1101-2020_10_26_351783 198 5 whether whether IN 10_1101-2020_10_26_351783 198 6 these these DT 10_1101-2020_10_26_351783 198 7 putative putative JJ 10_1101-2020_10_26_351783 198 8 gene gene NN 10_1101-2020_10_26_351783 198 9 - - HYPH 10_1101-2020_10_26_351783 198 10 risk risk NN 10_1101-2020_10_26_351783 198 11 factor factor NN 10_1101-2020_10_26_351783 198 12 associations association NNS 10_1101-2020_10_26_351783 198 13 could could MD 10_1101-2020_10_26_351783 198 14 be be VB 10_1101-2020_10_26_351783 198 15 validated validate VBN 10_1101-2020_10_26_351783 198 16 using use VBG 10_1101-2020_10_26_351783 198 17 an an DT 10_1101-2020_10_26_351783 198 18 independent independent JJ 10_1101-2020_10_26_351783 198 19 omics omic NNS 10_1101-2020_10_26_351783 198 20 dataset dataset VBN 10_1101-2020_10_26_351783 198 21 with with IN 10_1101-2020_10_26_351783 198 22 paired pair VBN 10_1101-2020_10_26_351783 198 23 risk risk NN 10_1101-2020_10_26_351783 198 24 factor factor NN 10_1101-2020_10_26_351783 198 25 associations association NNS 10_1101-2020_10_26_351783 198 26 . . . 10_1101-2020_10_26_351783 199 1 For for IN 10_1101-2020_10_26_351783 199 2 this this DT 10_1101-2020_10_26_351783 199 3 purpose purpose NN 10_1101-2020_10_26_351783 199 4 , , , 10_1101-2020_10_26_351783 199 5 we -PRON- PRP 10_1101-2020_10_26_351783 199 6 utilized utilize VBD 10_1101-2020_10_26_351783 199 7 methylation methylation NN 10_1101-2020_10_26_351783 199 8 arrays array NNS 10_1101-2020_10_26_351783 199 9 of of IN 10_1101-2020_10_26_351783 199 10 peripheral peripheral JJ 10_1101-2020_10_26_351783 199 11 blood blood NN 10_1101-2020_10_26_351783 199 12 from from IN 10_1101-2020_10_26_351783 199 13 139 139 CD 10_1101-2020_10_26_351783 199 14 MS MS NNP 10_1101-2020_10_26_351783 199 15 patients patient NNS 10_1101-2020_10_26_351783 199 16 and and CC 10_1101-2020_10_26_351783 199 17 140 140 CD 10_1101-2020_10_26_351783 199 18 controls control NNS 10_1101-2020_10_26_351783 199 19 , , , 10_1101-2020_10_26_351783 199 20 which which WDT 10_1101-2020_10_26_351783 199 21 have have VBP 10_1101-2020_10_26_351783 199 22 been be VBN 10_1101-2020_10_26_351783 199 23 described describe VBN 10_1101-2020_10_26_351783 199 24 previously[36 previously[36 NNP 10_1101-2020_10_26_351783 199 25 ] ] -RRB- 10_1101-2020_10_26_351783 199 26 . . . 10_1101-2020_10_26_351783 200 1 In in IN 10_1101-2020_10_26_351783 200 2 this this DT 10_1101-2020_10_26_351783 200 3 analysis analysis NN 10_1101-2020_10_26_351783 200 4 we -PRON- PRP 10_1101-2020_10_26_351783 200 5 also also RB 10_1101-2020_10_26_351783 200 6 considered consider VBD 10_1101-2020_10_26_351783 200 7 risk risk NN 10_1101-2020_10_26_351783 200 8 factor factor NN 10_1101-2020_10_26_351783 200 9 associations association NNS 10_1101-2020_10_26_351783 200 10 for for IN 10_1101-2020_10_26_351783 200 11 each each DT 10_1101-2020_10_26_351783 200 12 individual individual NN 10_1101-2020_10_26_351783 200 13 including include VBG 10_1101-2020_10_26_351783 200 14 age age NN 10_1101-2020_10_26_351783 200 15 , , , 10_1101-2020_10_26_351783 200 16 sex sex NN 10_1101-2020_10_26_351783 200 17 , , , 10_1101-2020_10_26_351783 200 18 BMI BMI NNP 10_1101-2020_10_26_351783 200 19 at at IN 10_1101-2020_10_26_351783 200 20 age age NN 10_1101-2020_10_26_351783 200 21 of of IN 10_1101-2020_10_26_351783 200 22 20 20 CD 10_1101-2020_10_26_351783 200 23 , , , 10_1101-2020_10_26_351783 200 24 smoking smoking NN 10_1101-2020_10_26_351783 200 25 , , , 10_1101-2020_10_26_351783 200 26 alcohol alcohol NN 10_1101-2020_10_26_351783 200 27 consumption consumption NN 10_1101-2020_10_26_351783 200 28 , , , 10_1101-2020_10_26_351783 200 29 sun sun NN 10_1101-2020_10_26_351783 200 30 exposure exposure NN 10_1101-2020_10_26_351783 200 31 , , , 10_1101-2020_10_26_351783 200 32 night night NN 10_1101-2020_10_26_351783 200 33 shift shift NN 10_1101-2020_10_26_351783 200 34 work work NN 10_1101-2020_10_26_351783 200 35 , , , 10_1101-2020_10_26_351783 200 36 contact contact NN 10_1101-2020_10_26_351783 200 37 with with IN 10_1101-2020_10_26_351783 200 38 organic organic JJ 10_1101-2020_10_26_351783 200 39 solvents solvent NNS 10_1101-2020_10_26_351783 200 40 . . . 10_1101-2020_10_26_351783 201 1 This this DT 10_1101-2020_10_26_351783 201 2 enabled enable VBD 10_1101-2020_10_26_351783 201 3 analysis analysis NN 10_1101-2020_10_26_351783 201 4 of of IN 10_1101-2020_10_26_351783 201 5 DMGs DMGs NNPS 10_1101-2020_10_26_351783 201 6 for for IN 10_1101-2020_10_26_351783 201 7 the the DT 10_1101-2020_10_26_351783 201 8 MS MS NNP 10_1101-2020_10_26_351783 201 9 and and CC 10_1101-2020_10_26_351783 201 10 risk risk NN 10_1101-2020_10_26_351783 201 11 factor factor NN 10_1101-2020_10_26_351783 201 12 status status NN 10_1101-2020_10_26_351783 201 13 as as IN 10_1101-2020_10_26_351783 201 14 covariates covariate NNS 10_1101-2020_10_26_351783 201 15 in in IN 10_1101-2020_10_26_351783 201 16 linear linear JJ 10_1101-2020_10_26_351783 201 17 mixed mixed JJ 10_1101-2020_10_26_351783 201 18 effect effect NN 10_1101-2020_10_26_351783 201 19 ( ( -LRB- 10_1101-2020_10_26_351783 201 20 which which WDT 10_1101-2020_10_26_351783 201 21 was be VBD 10_1101-2020_10_26_351783 201 22 not not RB 10_1101-2020_10_26_351783 201 23 certified certify VBN 10_1101-2020_10_26_351783 201 24 by by IN 10_1101-2020_10_26_351783 201 25 peer peer NN 10_1101-2020_10_26_351783 201 26 review review NN 10_1101-2020_10_26_351783 201 27 ) ) -RRB- 10_1101-2020_10_26_351783 201 28 is be VBZ 10_1101-2020_10_26_351783 201 29 the the DT 10_1101-2020_10_26_351783 201 30 author author NN 10_1101-2020_10_26_351783 201 31 / / SYM 10_1101-2020_10_26_351783 201 32 funder funder NN 10_1101-2020_10_26_351783 201 33 . . . 10_1101-2020_10_26_351783 202 1 All all DT 10_1101-2020_10_26_351783 202 2 rights right NNS 10_1101-2020_10_26_351783 202 3 reserved reserve VBD 10_1101-2020_10_26_351783 202 4 . . . 10_1101-2020_10_26_351783 203 1 No no DT 10_1101-2020_10_26_351783 203 2 reuse reuse NN 10_1101-2020_10_26_351783 203 3 allowed allow VBN 10_1101-2020_10_26_351783 203 4 without without IN 10_1101-2020_10_26_351783 203 5 permission permission NN 10_1101-2020_10_26_351783 203 6 . . . 10_1101-2020_10_26_351783 204 1 The the DT 10_1101-2020_10_26_351783 204 2 copyright copyright NN 10_1101-2020_10_26_351783 204 3 holder holder NN 10_1101-2020_10_26_351783 204 4 for for IN 10_1101-2020_10_26_351783 204 5 this this DT 10_1101-2020_10_26_351783 204 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 204 7 version version NN 10_1101-2020_10_26_351783 204 8 posted post VBD 10_1101-2020_10_26_351783 204 9 January January NNP 10_1101-2020_10_26_351783 204 10 6 6 CD 10_1101-2020_10_26_351783 204 11 , , , 10_1101-2020_10_26_351783 204 12 2021 2021 CD 10_1101-2020_10_26_351783 204 13 . . . 10_1101-2020_10_26_351783 204 14 ; ; : 10_1101-2020_10_26_351783 204 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 204 16 : : : 10_1101-2020_10_26_351783 204 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 204 18 preprint preprint NN 10_1101-2020_10_26_351783 204 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 204 20 14 14 CD 10_1101-2020_10_26_351783 204 21 analysis analysis NN 10_1101-2020_10_26_351783 204 22 . . . 10_1101-2020_10_26_351783 205 1 Indeed indeed RB 10_1101-2020_10_26_351783 205 2 , , , 10_1101-2020_10_26_351783 205 3 the the DT 10_1101-2020_10_26_351783 205 4 module module JJ 10_1101-2020_10_26_351783 205 5 genes gene NNS 10_1101-2020_10_26_351783 205 6 were be VBD 10_1101-2020_10_26_351783 205 7 highly highly RB 10_1101-2020_10_26_351783 205 8 significantly significantly RB 10_1101-2020_10_26_351783 205 9 enriched enrich VBN 10_1101-2020_10_26_351783 205 10 for for IN 10_1101-2020_10_26_351783 205 11 MS MS NNP 10_1101-2020_10_26_351783 205 12 ( ( -LRB- 10_1101-2020_10_26_351783 205 13 n n NNP 10_1101-2020_10_26_351783 205 14 = = SYM 10_1101-2020_10_26_351783 205 15 217 217 CD 10_1101-2020_10_26_351783 205 16 ; ; : 10_1101-2020_10_26_351783 205 17 permutation permutation NN 10_1101-2020_10_26_351783 205 18 test test NN 10_1101-2020_10_26_351783 205 19 P p NN 10_1101-2020_10_26_351783 205 20 = = SYM 10_1101-2020_10_26_351783 205 21 1.2 1.2 CD 10_1101-2020_10_26_351783 205 22 x x SYM 10_1101-2020_10_26_351783 205 23 10 10 CD 10_1101-2020_10_26_351783 205 24 - - SYM 10_1101-2020_10_26_351783 205 25 47 47 CD 10_1101-2020_10_26_351783 205 26 ) ) -RRB- 10_1101-2020_10_26_351783 205 27 , , , 10_1101-2020_10_26_351783 205 28 but but CC 10_1101-2020_10_26_351783 205 29 also also RB 10_1101-2020_10_26_351783 205 30 for for IN 10_1101-2020_10_26_351783 205 31 all all PDT 10_1101-2020_10_26_351783 205 32 the the DT 10_1101-2020_10_26_351783 205 33 tested test VBN 10_1101-2020_10_26_351783 205 34 risk risk NN 10_1101-2020_10_26_351783 205 35 factors factor NNS 10_1101-2020_10_26_351783 205 36 ( ( -LRB- 10_1101-2020_10_26_351783 205 37 EBV EBV NNP 10_1101-2020_10_26_351783 205 38 was be VBD 10_1101-2020_10_26_351783 205 39 not not RB 10_1101-2020_10_26_351783 205 40 included include VBN 10_1101-2020_10_26_351783 205 41 , , , 10_1101-2020_10_26_351783 205 42 Methods Methods NNP 10_1101-2020_10_26_351783 205 43 ) ) -RRB- 10_1101-2020_10_26_351783 205 44 and and CC 10_1101-2020_10_26_351783 205 45 non- non- NNP 10_1101-2020_10_26_351783 205 46 significantly significantly RB 10_1101-2020_10_26_351783 205 47 associated associate VBN 10_1101-2020_10_26_351783 205 48 to to IN 10_1101-2020_10_26_351783 205 49 age age NN 10_1101-2020_10_26_351783 205 50 and and CC 10_1101-2020_10_26_351783 205 51 sex sex NN 10_1101-2020_10_26_351783 205 52 having have VBG 10_1101-2020_10_26_351783 205 53 104 104 CD 10_1101-2020_10_26_351783 205 54 - - SYM 10_1101-2020_10_26_351783 205 55 135 135 CD 10_1101-2020_10_26_351783 205 56 of of IN 10_1101-2020_10_26_351783 205 57 the the DT 10_1101-2020_10_26_351783 205 58 genes gene NNS 10_1101-2020_10_26_351783 205 59 in in IN 10_1101-2020_10_26_351783 205 60 each each DT 10_1101-2020_10_26_351783 205 61 factor factor NN 10_1101-2020_10_26_351783 205 62 ( ( -LRB- 10_1101-2020_10_26_351783 205 63 3.9x10 3.9x10 CD 10_1101-2020_10_26_351783 205 64 - - SYM 10_1101-2020_10_26_351783 205 65 8 8 CD 10_1101-2020_10_26_351783 205 66 < < XX 10_1101-2020_10_26_351783 205 67 P p NN 10_1101-2020_10_26_351783 205 68 < < XX 10_1101-2020_10_26_351783 205 69 0.013 0.013 CD 10_1101-2020_10_26_351783 205 70 ; ; : 10_1101-2020_10_26_351783 205 71 Fig fig VB 10_1101-2020_10_26_351783 205 72 5b 5b NN 10_1101-2020_10_26_351783 205 73 ) ) -RRB- 10_1101-2020_10_26_351783 205 74 . . . 10_1101-2020_10_26_351783 206 1 Combining combine VBG 10_1101-2020_10_26_351783 206 2 all all PDT 10_1101-2020_10_26_351783 206 3 these these DT 10_1101-2020_10_26_351783 206 4 results result NNS 10_1101-2020_10_26_351783 206 5 we -PRON- PRP 10_1101-2020_10_26_351783 206 6 found find VBD 10_1101-2020_10_26_351783 206 7 90 90 CD 10_1101-2020_10_26_351783 206 8 of of IN 10_1101-2020_10_26_351783 206 9 the the DT 10_1101-2020_10_26_351783 206 10 220 220 CD 10_1101-2020_10_26_351783 206 11 module module JJ 10_1101-2020_10_26_351783 206 12 genes gene NNS 10_1101-2020_10_26_351783 206 13 to to TO 10_1101-2020_10_26_351783 206 14 be be VB 10_1101-2020_10_26_351783 206 15 associated associate VBN 10_1101-2020_10_26_351783 206 16 with with IN 10_1101-2020_10_26_351783 206 17 a a DT 10_1101-2020_10_26_351783 206 18 risk risk NN 10_1101-2020_10_26_351783 206 19 factors factor NNS 10_1101-2020_10_26_351783 206 20 from from IN 10_1101-2020_10_26_351783 206 21 both both CC 10_1101-2020_10_26_351783 206 22 the the DT 10_1101-2020_10_26_351783 206 23 risk risk NN 10_1101-2020_10_26_351783 206 24 factor factor NN 10_1101-2020_10_26_351783 206 25 studies study NNS 10_1101-2020_10_26_351783 206 26 , , , 10_1101-2020_10_26_351783 206 27 25 25 CD 10_1101-2020_10_26_351783 206 28 genes gene NNS 10_1101-2020_10_26_351783 206 29 were be VBD 10_1101-2020_10_26_351783 206 30 associated associate VBN 10_1101-2020_10_26_351783 206 31 with with IN 10_1101-2020_10_26_351783 206 32 two two CD 10_1101-2020_10_26_351783 206 33 risk risk NN 10_1101-2020_10_26_351783 206 34 factors factor NNS 10_1101-2020_10_26_351783 206 35 , , , 10_1101-2020_10_26_351783 206 36 and and CC 10_1101-2020_10_26_351783 206 37 seven seven CD 10_1101-2020_10_26_351783 206 38 genes gene NNS 10_1101-2020_10_26_351783 206 39 were be VBD 10_1101-2020_10_26_351783 206 40 associated associate VBN 10_1101-2020_10_26_351783 206 41 with with IN 10_1101-2020_10_26_351783 206 42 three three CD 10_1101-2020_10_26_351783 206 43 risk risk NN 10_1101-2020_10_26_351783 206 44 factors factor NNS 10_1101-2020_10_26_351783 206 45 ( ( -LRB- 10_1101-2020_10_26_351783 206 46 CSK CSK NNP 10_1101-2020_10_26_351783 206 47 , , , 10_1101-2020_10_26_351783 206 48 PRKCA PRKCA NNP 10_1101-2020_10_26_351783 206 49 , , , 10_1101-2020_10_26_351783 206 50 PRKCZ PRKCZ NNP 10_1101-2020_10_26_351783 206 51 , , , 10_1101-2020_10_26_351783 206 52 RUNX1 runx1 NN 10_1101-2020_10_26_351783 206 53 , , , 10_1101-2020_10_26_351783 206 54 RUNX3 runx3 NN 10_1101-2020_10_26_351783 206 55 , , , 10_1101-2020_10_26_351783 206 56 STAT5A STAT5A NNP 10_1101-2020_10_26_351783 206 57 , , , 10_1101-2020_10_26_351783 206 58 and and CC 10_1101-2020_10_26_351783 206 59 SYNJ2 synj2 NN 10_1101-2020_10_26_351783 206 60 ) ) -RRB- 10_1101-2020_10_26_351783 206 61 ( ( -LRB- 10_1101-2020_10_26_351783 206 62 Fig fig NN 10_1101-2020_10_26_351783 206 63 . . . 10_1101-2020_10_26_351783 207 1 5c 5c LS 10_1101-2020_10_26_351783 207 2 ) ) -RRB- 10_1101-2020_10_26_351783 207 3 . . . 10_1101-2020_10_26_351783 208 1 These these DT 10_1101-2020_10_26_351783 208 2 associations association NNS 10_1101-2020_10_26_351783 208 3 suggest suggest VBP 10_1101-2020_10_26_351783 208 4 that that IN 10_1101-2020_10_26_351783 208 5 the the DT 10_1101-2020_10_26_351783 208 6 multi multi JJ 10_1101-2020_10_26_351783 208 7 - - JJ 10_1101-2020_10_26_351783 208 8 omics omics JJ 10_1101-2020_10_26_351783 208 9 module module NN 10_1101-2020_10_26_351783 208 10 is be VBZ 10_1101-2020_10_26_351783 208 11 capturing capture VBG 10_1101-2020_10_26_351783 208 12 a a DT 10_1101-2020_10_26_351783 208 13 key key JJ 10_1101-2020_10_26_351783 208 14 disease disease NN 10_1101-2020_10_26_351783 208 15 network network NN 10_1101-2020_10_26_351783 208 16 with with IN 10_1101-2020_10_26_351783 208 17 both both CC 10_1101-2020_10_26_351783 208 18 genetically genetically RB 10_1101-2020_10_26_351783 208 19 and and CC 10_1101-2020_10_26_351783 208 20 epigenetically epigenetically RB 10_1101-2020_10_26_351783 208 21 driven drive VBN 10_1101-2020_10_26_351783 208 22 alterations alteration NNS 10_1101-2020_10_26_351783 208 23 , , , 10_1101-2020_10_26_351783 208 24 thereby thereby RB 10_1101-2020_10_26_351783 208 25 providing provide VBG 10_1101-2020_10_26_351783 208 26 the the DT 10_1101-2020_10_26_351783 208 27 possibility possibility NN 10_1101-2020_10_26_351783 208 28 to to TO 10_1101-2020_10_26_351783 208 29 use use VB 10_1101-2020_10_26_351783 208 30 it -PRON- PRP 10_1101-2020_10_26_351783 208 31 to to TO 10_1101-2020_10_26_351783 208 32 identify identify VB 10_1101-2020_10_26_351783 208 33 potential potential JJ 10_1101-2020_10_26_351783 208 34 novel novel JJ 10_1101-2020_10_26_351783 208 35 biomarkers biomarker NNS 10_1101-2020_10_26_351783 208 36 or or CC 10_1101-2020_10_26_351783 208 37 therapeutic therapeutic JJ 10_1101-2020_10_26_351783 208 38 targets target NNS 10_1101-2020_10_26_351783 208 39 for for IN 10_1101-2020_10_26_351783 208 40 MS MS NNP 10_1101-2020_10_26_351783 208 41 . . . 10_1101-2020_10_26_351783 208 42 � � NNP 10_1101-2020_10_26_351783 208 43 ( ( -LRB- 10_1101-2020_10_26_351783 208 44 which which WDT 10_1101-2020_10_26_351783 208 45 was be VBD 10_1101-2020_10_26_351783 208 46 not not RB 10_1101-2020_10_26_351783 208 47 certified certify VBN 10_1101-2020_10_26_351783 208 48 by by IN 10_1101-2020_10_26_351783 208 49 peer peer NN 10_1101-2020_10_26_351783 208 50 review review NN 10_1101-2020_10_26_351783 208 51 ) ) -RRB- 10_1101-2020_10_26_351783 208 52 is be VBZ 10_1101-2020_10_26_351783 208 53 the the DT 10_1101-2020_10_26_351783 208 54 author author NN 10_1101-2020_10_26_351783 208 55 / / SYM 10_1101-2020_10_26_351783 208 56 funder funder NN 10_1101-2020_10_26_351783 208 57 . . . 10_1101-2020_10_26_351783 209 1 All all DT 10_1101-2020_10_26_351783 209 2 rights right NNS 10_1101-2020_10_26_351783 209 3 reserved reserve VBD 10_1101-2020_10_26_351783 209 4 . . . 10_1101-2020_10_26_351783 210 1 No no DT 10_1101-2020_10_26_351783 210 2 reuse reuse NN 10_1101-2020_10_26_351783 210 3 allowed allow VBN 10_1101-2020_10_26_351783 210 4 without without IN 10_1101-2020_10_26_351783 210 5 permission permission NN 10_1101-2020_10_26_351783 210 6 . . . 10_1101-2020_10_26_351783 211 1 The the DT 10_1101-2020_10_26_351783 211 2 copyright copyright NN 10_1101-2020_10_26_351783 211 3 holder holder NN 10_1101-2020_10_26_351783 211 4 for for IN 10_1101-2020_10_26_351783 211 5 this this DT 10_1101-2020_10_26_351783 211 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 211 7 version version NN 10_1101-2020_10_26_351783 211 8 posted post VBD 10_1101-2020_10_26_351783 211 9 January January NNP 10_1101-2020_10_26_351783 211 10 6 6 CD 10_1101-2020_10_26_351783 211 11 , , , 10_1101-2020_10_26_351783 211 12 2021 2021 CD 10_1101-2020_10_26_351783 211 13 . . . 10_1101-2020_10_26_351783 211 14 ; ; : 10_1101-2020_10_26_351783 211 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 211 16 : : : 10_1101-2020_10_26_351783 211 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 211 18 preprint preprint NN 10_1101-2020_10_26_351783 211 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 211 20 15 15 CD 10_1101-2020_10_26_351783 211 21 DISCUSSION discussion NN 10_1101-2020_10_26_351783 211 22 The the DT 10_1101-2020_10_26_351783 211 23 analysis analysis NN 10_1101-2020_10_26_351783 211 24 of of IN 10_1101-2020_10_26_351783 211 25 case case NN 10_1101-2020_10_26_351783 211 26 control control NNP 10_1101-2020_10_26_351783 211 27 data datum NNS 10_1101-2020_10_26_351783 211 28 in in IN 10_1101-2020_10_26_351783 211 29 the the DT 10_1101-2020_10_26_351783 211 30 context context NN 10_1101-2020_10_26_351783 211 31 of of IN 10_1101-2020_10_26_351783 211 32 networks network NNS 10_1101-2020_10_26_351783 211 33 has have VBZ 10_1101-2020_10_26_351783 211 34 gained gain VBN 10_1101-2020_10_26_351783 211 35 increased increase VBN 10_1101-2020_10_26_351783 211 36 interest interest NN 10_1101-2020_10_26_351783 211 37 to to TO 10_1101-2020_10_26_351783 211 38 detect detect VB 10_1101-2020_10_26_351783 211 39 consistent consistent JJ 10_1101-2020_10_26_351783 211 40 robust robust JJ 10_1101-2020_10_26_351783 211 41 gene gene NN 10_1101-2020_10_26_351783 211 42 signatures signature NNS 10_1101-2020_10_26_351783 211 43 of of IN 10_1101-2020_10_26_351783 211 44 individual individual JJ 10_1101-2020_10_26_351783 211 45 diseases disease NNS 10_1101-2020_10_26_351783 211 46 . . . 10_1101-2020_10_26_351783 212 1 The the DT 10_1101-2020_10_26_351783 212 2 application application NN 10_1101-2020_10_26_351783 212 3 of of IN 10_1101-2020_10_26_351783 212 4 disease disease NN 10_1101-2020_10_26_351783 212 5 modules module NNS 10_1101-2020_10_26_351783 212 6 might may MD 10_1101-2020_10_26_351783 212 7 vary vary VB 10_1101-2020_10_26_351783 212 8 for for IN 10_1101-2020_10_26_351783 212 9 different different JJ 10_1101-2020_10_26_351783 212 10 researchers researcher NNS 10_1101-2020_10_26_351783 212 11 , , , 10_1101-2020_10_26_351783 212 12 but but CC 10_1101-2020_10_26_351783 212 13 here here RB 10_1101-2020_10_26_351783 212 14 we -PRON- PRP 10_1101-2020_10_26_351783 212 15 systematically systematically RB 10_1101-2020_10_26_351783 212 16 aimed aim VBD 10_1101-2020_10_26_351783 212 17 at at IN 10_1101-2020_10_26_351783 212 18 the the DT 10_1101-2020_10_26_351783 212 19 detection detection NN 10_1101-2020_10_26_351783 212 20 of of IN 10_1101-2020_10_26_351783 212 21 disease disease NN 10_1101-2020_10_26_351783 212 22 genes gene NNS 10_1101-2020_10_26_351783 212 23 supported support VBN 10_1101-2020_10_26_351783 212 24 by by IN 10_1101-2020_10_26_351783 212 25 genetic genetic NNP 10_1101-2020_10_26_351783 212 26 association association NNP 10_1101-2020_10_26_351783 212 27 . . . 10_1101-2020_10_26_351783 213 1 For for IN 10_1101-2020_10_26_351783 213 2 this this DT 10_1101-2020_10_26_351783 213 3 purpose purpose NN 10_1101-2020_10_26_351783 213 4 , , , 10_1101-2020_10_26_351783 213 5 our -PRON- PRP$ 10_1101-2020_10_26_351783 213 6 study study NN 10_1101-2020_10_26_351783 213 7 of of IN 10_1101-2020_10_26_351783 213 8 the the DT 10_1101-2020_10_26_351783 213 9 transcriptome transcriptome JJ 10_1101-2020_10_26_351783 213 10 and and CC 10_1101-2020_10_26_351783 213 11 methylome methylome JJ 10_1101-2020_10_26_351783 213 12 profiles profile NNS 10_1101-2020_10_26_351783 213 13 of of IN 10_1101-2020_10_26_351783 213 14 19 19 CD 10_1101-2020_10_26_351783 213 15 diseases disease NNS 10_1101-2020_10_26_351783 213 16 showed show VBD 10_1101-2020_10_26_351783 213 17 significant significant JJ 10_1101-2020_10_26_351783 213 18 GWAS GWAS NNP 10_1101-2020_10_26_351783 213 19 enrichments enrichment NNS 10_1101-2020_10_26_351783 213 20 for for IN 10_1101-2020_10_26_351783 213 21 several several JJ 10_1101-2020_10_26_351783 213 22 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 213 23 and and CC 10_1101-2020_10_26_351783 213 24 heart heart NN 10_1101-2020_10_26_351783 213 25 diseases disease NNS 10_1101-2020_10_26_351783 213 26 , , , 10_1101-2020_10_26_351783 213 27 while while IN 10_1101-2020_10_26_351783 213 28 psychiatric psychiatric JJ 10_1101-2020_10_26_351783 213 29 disorders disorder NNS 10_1101-2020_10_26_351783 213 30 showed show VBD 10_1101-2020_10_26_351783 213 31 no no DT 10_1101-2020_10_26_351783 213 32 enrichments enrichment NNS 10_1101-2020_10_26_351783 213 33 and and CC 10_1101-2020_10_26_351783 213 34 might may MD 10_1101-2020_10_26_351783 213 35 not not RB 10_1101-2020_10_26_351783 213 36 be be VB 10_1101-2020_10_26_351783 213 37 suitable suitable JJ 10_1101-2020_10_26_351783 213 38 for for IN 10_1101-2020_10_26_351783 213 39 GWAS GWAS NNP 10_1101-2020_10_26_351783 213 40 validation validation NN 10_1101-2020_10_26_351783 213 41 of of IN 10_1101-2020_10_26_351783 213 42 modules module NNS 10_1101-2020_10_26_351783 213 43 , , , 10_1101-2020_10_26_351783 213 44 potentially potentially RB 10_1101-2020_10_26_351783 213 45 due due JJ 10_1101-2020_10_26_351783 213 46 to to IN 10_1101-2020_10_26_351783 213 47 differences difference NNS 10_1101-2020_10_26_351783 213 48 in in IN 10_1101-2020_10_26_351783 213 49 affected affected JJ 10_1101-2020_10_26_351783 213 50 tissue tissue NN 10_1101-2020_10_26_351783 213 51 types type NNS 10_1101-2020_10_26_351783 213 52 and and CC 10_1101-2020_10_26_351783 213 53 sampling sampling NN 10_1101-2020_10_26_351783 213 54 points point NNS 10_1101-2020_10_26_351783 213 55 . . . 10_1101-2020_10_26_351783 214 1 However however RB 10_1101-2020_10_26_351783 214 2 , , , 10_1101-2020_10_26_351783 214 3 analysis analysis NN 10_1101-2020_10_26_351783 214 4 of of IN 10_1101-2020_10_26_351783 214 5 the the DT 10_1101-2020_10_26_351783 214 6 significant significant JJ 10_1101-2020_10_26_351783 214 7 results result NNS 10_1101-2020_10_26_351783 214 8 showed show VBD 10_1101-2020_10_26_351783 214 9 that that IN 10_1101-2020_10_26_351783 214 10 methods method NNS 10_1101-2020_10_26_351783 214 11 based base VBN 10_1101-2020_10_26_351783 214 12 of of IN 10_1101-2020_10_26_351783 214 13 differentially differentially RB 10_1101-2020_10_26_351783 214 14 expressed express VBN 10_1101-2020_10_26_351783 214 15 cliques clique NNS 10_1101-2020_10_26_351783 214 16 in in IN 10_1101-2020_10_26_351783 214 17 the the DT 10_1101-2020_10_26_351783 214 18 protein protein NN 10_1101-2020_10_26_351783 214 19 - - HYPH 10_1101-2020_10_26_351783 214 20 protein protein NN 10_1101-2020_10_26_351783 214 21 interaction interaction NN 10_1101-2020_10_26_351783 214 22 network network NN 10_1101-2020_10_26_351783 214 23 demonstrated demonstrate VBD 10_1101-2020_10_26_351783 214 24 the the DT 10_1101-2020_10_26_351783 214 25 strongest strong JJS 10_1101-2020_10_26_351783 214 26 enrichments enrichment NNS 10_1101-2020_10_26_351783 214 27 ( ( -LRB- 10_1101-2020_10_26_351783 214 28 highest high JJS 10_1101-2020_10_26_351783 214 29 scoring score VBG 10_1101-2020_10_26_351783 214 30 for for IN 10_1101-2020_10_26_351783 214 31 Clique Clique NNP 10_1101-2020_10_26_351783 214 32 SuM sum NN 10_1101-2020_10_26_351783 214 33 ) ) -RRB- 10_1101-2020_10_26_351783 214 34 , , , 10_1101-2020_10_26_351783 214 35 while while IN 10_1101-2020_10_26_351783 214 36 those those DT 10_1101-2020_10_26_351783 214 37 based base VBN 10_1101-2020_10_26_351783 214 38 primarily primarily RB 10_1101-2020_10_26_351783 214 39 on on IN 10_1101-2020_10_26_351783 214 40 correlations correlation NNS 10_1101-2020_10_26_351783 214 41 , , , 10_1101-2020_10_26_351783 214 42 like like IN 10_1101-2020_10_26_351783 214 43 WGCNA WGCNA NNP 10_1101-2020_10_26_351783 214 44 , , , 10_1101-2020_10_26_351783 214 45 showed show VBD 10_1101-2020_10_26_351783 214 46 weak weak JJ 10_1101-2020_10_26_351783 214 47 enrichments enrichment NNS 10_1101-2020_10_26_351783 214 48 . . . 10_1101-2020_10_26_351783 215 1 A a DT 10_1101-2020_10_26_351783 215 2 potential potential JJ 10_1101-2020_10_26_351783 215 3 reason reason NN 10_1101-2020_10_26_351783 215 4 for for IN 10_1101-2020_10_26_351783 215 5 this this DT 10_1101-2020_10_26_351783 215 6 could could MD 10_1101-2020_10_26_351783 215 7 be be VB 10_1101-2020_10_26_351783 215 8 that that IN 10_1101-2020_10_26_351783 215 9 GWAS GWAS NNP 10_1101-2020_10_26_351783 215 10 has have VBZ 10_1101-2020_10_26_351783 215 11 shown show VBN 10_1101-2020_10_26_351783 215 12 to to TO 10_1101-2020_10_26_351783 215 13 be be VB 10_1101-2020_10_26_351783 215 14 mostly mostly RB 10_1101-2020_10_26_351783 215 15 associated associate VBN 10_1101-2020_10_26_351783 215 16 to to IN 10_1101-2020_10_26_351783 215 17 the the DT 10_1101-2020_10_26_351783 215 18 central central JJ 10_1101-2020_10_26_351783 215 19 genes gene NNS 10_1101-2020_10_26_351783 215 20 of of IN 10_1101-2020_10_26_351783 215 21 the the DT 10_1101-2020_10_26_351783 215 22 protein protein NN 10_1101-2020_10_26_351783 215 23 - - HYPH 10_1101-2020_10_26_351783 215 24 protein protein NN 10_1101-2020_10_26_351783 215 25 interaction interaction NN 10_1101-2020_10_26_351783 215 26 ( ( -LRB- 10_1101-2020_10_26_351783 215 27 PPI PPI NNP 10_1101-2020_10_26_351783 215 28 ) ) -RRB- 10_1101-2020_10_26_351783 215 29 network network NN 10_1101-2020_10_26_351783 215 30 , , , 10_1101-2020_10_26_351783 215 31 but but CC 10_1101-2020_10_26_351783 215 32 our -PRON- PRP$ 10_1101-2020_10_26_351783 215 33 analysis analysis NN 10_1101-2020_10_26_351783 215 34 demonstrated demonstrate VBD 10_1101-2020_10_26_351783 215 35 that that IN 10_1101-2020_10_26_351783 215 36 the the DT 10_1101-2020_10_26_351783 215 37 correlation correlation NN 10_1101-2020_10_26_351783 215 38 between between IN 10_1101-2020_10_26_351783 215 39 GWAS GWAS NNP 10_1101-2020_10_26_351783 215 40 enrichment enrichment NN 10_1101-2020_10_26_351783 215 41 and and CC 10_1101-2020_10_26_351783 215 42 centrality centrality NN 10_1101-2020_10_26_351783 215 43 was be VBD 10_1101-2020_10_26_351783 215 44 non non JJ 10_1101-2020_10_26_351783 215 45 - - JJ 10_1101-2020_10_26_351783 215 46 significant significant JJ 10_1101-2020_10_26_351783 215 47 . . . 10_1101-2020_10_26_351783 216 1 We -PRON- PRP 10_1101-2020_10_26_351783 216 2 also also RB 10_1101-2020_10_26_351783 216 3 tested test VBD 10_1101-2020_10_26_351783 216 4 whether whether IN 10_1101-2020_10_26_351783 216 5 there there EX 10_1101-2020_10_26_351783 216 6 was be VBD 10_1101-2020_10_26_351783 216 7 an an DT 10_1101-2020_10_26_351783 216 8 improvement improvement NN 10_1101-2020_10_26_351783 216 9 using use VBG 10_1101-2020_10_26_351783 216 10 consensus consensus NN 10_1101-2020_10_26_351783 216 11 approaches approach NNS 10_1101-2020_10_26_351783 216 12 that that WDT 10_1101-2020_10_26_351783 216 13 counted count VBD 10_1101-2020_10_26_351783 216 14 the the DT 10_1101-2020_10_26_351783 216 15 frequency frequency NN 10_1101-2020_10_26_351783 216 16 of of IN 10_1101-2020_10_26_351783 216 17 the the DT 10_1101-2020_10_26_351783 216 18 result result NN 10_1101-2020_10_26_351783 216 19 of of IN 10_1101-2020_10_26_351783 216 20 multiple multiple JJ 10_1101-2020_10_26_351783 216 21 methods method NNS 10_1101-2020_10_26_351783 216 22 but but CC 10_1101-2020_10_26_351783 216 23 found find VBD 10_1101-2020_10_26_351783 216 24 this this DT 10_1101-2020_10_26_351783 216 25 not not RB 10_1101-2020_10_26_351783 216 26 to to TO 10_1101-2020_10_26_351783 216 27 increase increase VB 10_1101-2020_10_26_351783 216 28 performance performance NN 10_1101-2020_10_26_351783 216 29 . . . 10_1101-2020_10_26_351783 217 1 Moreover moreover RB 10_1101-2020_10_26_351783 217 2 , , , 10_1101-2020_10_26_351783 217 3 we -PRON- PRP 10_1101-2020_10_26_351783 217 4 tested test VBD 10_1101-2020_10_26_351783 217 5 the the DT 10_1101-2020_10_26_351783 217 6 same same JJ 10_1101-2020_10_26_351783 217 7 strategy strategy NN 10_1101-2020_10_26_351783 217 8 on on IN 10_1101-2020_10_26_351783 217 9 a a DT 10_1101-2020_10_26_351783 217 10 set set NN 10_1101-2020_10_26_351783 217 11 of of IN 10_1101-2020_10_26_351783 217 12 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 217 13 , , , 10_1101-2020_10_26_351783 217 14 glycemic glycemic JJ 10_1101-2020_10_26_351783 217 15 , , , 10_1101-2020_10_26_351783 217 16 and and CC 10_1101-2020_10_26_351783 217 17 autoimmune autoimmune JJ 10_1101-2020_10_26_351783 217 18 methylation methylation NN 10_1101-2020_10_26_351783 217 19 datasets dataset NNS 10_1101-2020_10_26_351783 217 20 and and CC 10_1101-2020_10_26_351783 217 21 found find VBD 10_1101-2020_10_26_351783 217 22 similar similar JJ 10_1101-2020_10_26_351783 217 23 results result NNS 10_1101-2020_10_26_351783 217 24 . . . 10_1101-2020_10_26_351783 218 1 We -PRON- PRP 10_1101-2020_10_26_351783 218 2 would would MD 10_1101-2020_10_26_351783 218 3 like like VB 10_1101-2020_10_26_351783 218 4 to to TO 10_1101-2020_10_26_351783 218 5 emphasize emphasize VB 10_1101-2020_10_26_351783 218 6 that that DT 10_1101-2020_10_26_351783 218 7 , , , 10_1101-2020_10_26_351783 218 8 rather rather RB 10_1101-2020_10_26_351783 218 9 than than IN 10_1101-2020_10_26_351783 218 10 scoring score VBG 10_1101-2020_10_26_351783 218 11 a a DT 10_1101-2020_10_26_351783 218 12 single single JJ 10_1101-2020_10_26_351783 218 13 best good JJS 10_1101-2020_10_26_351783 218 14 working working NN 10_1101-2020_10_26_351783 218 15 method method NN 10_1101-2020_10_26_351783 218 16 , , , 10_1101-2020_10_26_351783 218 17 our -PRON- PRP$ 10_1101-2020_10_26_351783 218 18 result result NN 10_1101-2020_10_26_351783 218 19 is be VBZ 10_1101-2020_10_26_351783 218 20 a a DT 10_1101-2020_10_26_351783 218 21 pipeline pipeline NN 10_1101-2020_10_26_351783 218 22 for for IN 10_1101-2020_10_26_351783 218 23 evaluating evaluate VBG 10_1101-2020_10_26_351783 218 24 modules module NNS 10_1101-2020_10_26_351783 218 25 using use VBG 10_1101-2020_10_26_351783 218 26 independent independent JJ 10_1101-2020_10_26_351783 218 27 high high JJ 10_1101-2020_10_26_351783 218 28 - - HYPH 10_1101-2020_10_26_351783 218 29 throughput throughput NN 10_1101-2020_10_26_351783 218 30 enrichments enrichment NNS 10_1101-2020_10_26_351783 218 31 . . . 10_1101-2020_10_26_351783 219 1 The the DT 10_1101-2020_10_26_351783 219 2 work work NN 10_1101-2020_10_26_351783 219 3 on on IN 10_1101-2020_10_26_351783 219 4 transcription transcription NN 10_1101-2020_10_26_351783 219 5 and and CC 10_1101-2020_10_26_351783 219 6 methylation methylation NN 10_1101-2020_10_26_351783 219 7 datasets dataset NNS 10_1101-2020_10_26_351783 219 8 suggested suggest VBD 10_1101-2020_10_26_351783 219 9 that that IN 10_1101-2020_10_26_351783 219 10 MS MS NNP 10_1101-2020_10_26_351783 219 11 is be VBZ 10_1101-2020_10_26_351783 219 12 a a DT 10_1101-2020_10_26_351783 219 13 disease disease NN 10_1101-2020_10_26_351783 219 14 highly highly RB 10_1101-2020_10_26_351783 219 15 enriched enrich VBN 10_1101-2020_10_26_351783 219 16 for for IN 10_1101-2020_10_26_351783 219 17 GWAS GWAS NNP 10_1101-2020_10_26_351783 219 18 , , , 10_1101-2020_10_26_351783 219 19 and and CC 10_1101-2020_10_26_351783 219 20 we -PRON- PRP 10_1101-2020_10_26_351783 219 21 therefore therefore RB 10_1101-2020_10_26_351783 219 22 tested test VBD 10_1101-2020_10_26_351783 219 23 if if IN 10_1101-2020_10_26_351783 219 24 increased increase VBN 10_1101-2020_10_26_351783 219 25 enrichments enrichment NNS 10_1101-2020_10_26_351783 219 26 could could MD 10_1101-2020_10_26_351783 219 27 be be VB 10_1101-2020_10_26_351783 219 28 derived derive VBN 10_1101-2020_10_26_351783 219 29 by by IN 10_1101-2020_10_26_351783 219 30 their -PRON- PRP$ 10_1101-2020_10_26_351783 219 31 integration integration NN 10_1101-2020_10_26_351783 219 32 . . . 10_1101-2020_10_26_351783 220 1 We -PRON- PRP 10_1101-2020_10_26_351783 220 2 found find VBD 10_1101-2020_10_26_351783 220 3 20 20 CD 10_1101-2020_10_26_351783 220 4 publicly publicly RB 10_1101-2020_10_26_351783 220 5 available available JJ 10_1101-2020_10_26_351783 220 6 datasets dataset NNS 10_1101-2020_10_26_351783 220 7 and and CC 10_1101-2020_10_26_351783 220 8 run run VB 10_1101-2020_10_26_351783 220 9 assessment assessment NN 10_1101-2020_10_26_351783 220 10 for for IN 10_1101-2020_10_26_351783 220 11 both both DT 10_1101-2020_10_26_351783 220 12 omics omic NNS 10_1101-2020_10_26_351783 220 13 independently independently RB 10_1101-2020_10_26_351783 220 14 , , , 10_1101-2020_10_26_351783 220 15 which which WDT 10_1101-2020_10_26_351783 220 16 again again RB 10_1101-2020_10_26_351783 220 17 showed show VBD 10_1101-2020_10_26_351783 220 18 Clique Clique NNP 10_1101-2020_10_26_351783 220 19 SuM sum NN 10_1101-2020_10_26_351783 220 20 to to TO 10_1101-2020_10_26_351783 220 21 score score VB 10_1101-2020_10_26_351783 220 22 highest highest RBS 10_1101-2020_10_26_351783 220 23 . . . 10_1101-2020_10_26_351783 221 1 We -PRON- PRP 10_1101-2020_10_26_351783 221 2 then then RB 10_1101-2020_10_26_351783 221 3 tested test VBD 10_1101-2020_10_26_351783 221 4 if if IN 10_1101-2020_10_26_351783 221 5 improved improve VBN 10_1101-2020_10_26_351783 221 6 results result NNS 10_1101-2020_10_26_351783 221 7 could could MD 10_1101-2020_10_26_351783 221 8 be be VB 10_1101-2020_10_26_351783 221 9 obtained obtain VBN 10_1101-2020_10_26_351783 221 10 using use VBG 10_1101-2020_10_26_351783 221 11 modules module NNS 10_1101-2020_10_26_351783 221 12 from from IN 10_1101-2020_10_26_351783 221 13 multiple multiple JJ 10_1101-2020_10_26_351783 221 14 datasets dataset NNS 10_1101-2020_10_26_351783 221 15 of of IN 10_1101-2020_10_26_351783 221 16 these these DT 10_1101-2020_10_26_351783 221 17 two two CD 10_1101-2020_10_26_351783 221 18 omics omic NNS 10_1101-2020_10_26_351783 221 19 using use VBG 10_1101-2020_10_26_351783 221 20 consensus consensus NN 10_1101-2020_10_26_351783 221 21 modules module NNS 10_1101-2020_10_26_351783 221 22 from from IN 10_1101-2020_10_26_351783 221 23 Clique Clique NNP 10_1101-2020_10_26_351783 221 24 SuM. SuM. NNP 10_1101-2020_10_26_351783 222 1 This this DT 10_1101-2020_10_26_351783 222 2 resulted result VBD 10_1101-2020_10_26_351783 222 3 in in IN 10_1101-2020_10_26_351783 222 4 a a DT 10_1101-2020_10_26_351783 222 5 module module NN 10_1101-2020_10_26_351783 222 6 of of IN 10_1101-2020_10_26_351783 222 7 220 220 CD 10_1101-2020_10_26_351783 222 8 genes gene NNS 10_1101-2020_10_26_351783 222 9 highly highly RB 10_1101-2020_10_26_351783 222 10 enriched enrich VBN 10_1101-2020_10_26_351783 222 11 for for IN 10_1101-2020_10_26_351783 222 12 GWAS GWAS NNP 10_1101-2020_10_26_351783 222 13 ( ( -LRB- 10_1101-2020_10_26_351783 222 14 P p NN 10_1101-2020_10_26_351783 222 15 = = SYM 10_1101-2020_10_26_351783 222 16 8.8 8.8 CD 10_1101-2020_10_26_351783 222 17 x x SYM 10_1101-2020_10_26_351783 222 18 10 10 CD 10_1101-2020_10_26_351783 222 19 - - SYM 10_1101-2020_10_26_351783 222 20 9 9 CD 10_1101-2020_10_26_351783 222 21 ) ) -RRB- 10_1101-2020_10_26_351783 222 22 . . . 10_1101-2020_10_26_351783 223 1 The the DT 10_1101-2020_10_26_351783 223 2 multi- multi- JJ 10_1101-2020_10_26_351783 223 3 omic omic JJ 10_1101-2020_10_26_351783 223 4 module module NN 10_1101-2020_10_26_351783 223 5 was be VBD 10_1101-2020_10_26_351783 223 6 highly highly RB 10_1101-2020_10_26_351783 223 7 enriched enrich VBN 10_1101-2020_10_26_351783 223 8 in in IN 10_1101-2020_10_26_351783 223 9 immune immune NN 10_1101-2020_10_26_351783 223 10 - - HYPH 10_1101-2020_10_26_351783 223 11 associated associate VBN 10_1101-2020_10_26_351783 223 12 pathways pathway NNS 10_1101-2020_10_26_351783 223 13 , , , 10_1101-2020_10_26_351783 223 14 such such JJ 10_1101-2020_10_26_351783 223 15 as as IN 10_1101-2020_10_26_351783 223 16 T T NNP 10_1101-2020_10_26_351783 223 17 cell cell NN 10_1101-2020_10_26_351783 223 18 and and CC 10_1101-2020_10_26_351783 223 19 B b NN 10_1101-2020_10_26_351783 223 20 cell cell NN 10_1101-2020_10_26_351783 223 21 receptor receptor NN 10_1101-2020_10_26_351783 223 22 ( ( -LRB- 10_1101-2020_10_26_351783 223 23 which which WDT 10_1101-2020_10_26_351783 223 24 was be VBD 10_1101-2020_10_26_351783 223 25 not not RB 10_1101-2020_10_26_351783 223 26 certified certify VBN 10_1101-2020_10_26_351783 223 27 by by IN 10_1101-2020_10_26_351783 223 28 peer peer NN 10_1101-2020_10_26_351783 223 29 review review NN 10_1101-2020_10_26_351783 223 30 ) ) -RRB- 10_1101-2020_10_26_351783 223 31 is be VBZ 10_1101-2020_10_26_351783 223 32 the the DT 10_1101-2020_10_26_351783 223 33 author author NN 10_1101-2020_10_26_351783 223 34 / / SYM 10_1101-2020_10_26_351783 223 35 funder funder NN 10_1101-2020_10_26_351783 223 36 . . . 10_1101-2020_10_26_351783 224 1 All all DT 10_1101-2020_10_26_351783 224 2 rights right NNS 10_1101-2020_10_26_351783 224 3 reserved reserve VBD 10_1101-2020_10_26_351783 224 4 . . . 10_1101-2020_10_26_351783 225 1 No no DT 10_1101-2020_10_26_351783 225 2 reuse reuse NN 10_1101-2020_10_26_351783 225 3 allowed allow VBN 10_1101-2020_10_26_351783 225 4 without without IN 10_1101-2020_10_26_351783 225 5 permission permission NN 10_1101-2020_10_26_351783 225 6 . . . 10_1101-2020_10_26_351783 226 1 The the DT 10_1101-2020_10_26_351783 226 2 copyright copyright NN 10_1101-2020_10_26_351783 226 3 holder holder NN 10_1101-2020_10_26_351783 226 4 for for IN 10_1101-2020_10_26_351783 226 5 this this DT 10_1101-2020_10_26_351783 226 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 226 7 version version NN 10_1101-2020_10_26_351783 226 8 posted post VBD 10_1101-2020_10_26_351783 226 9 January January NNP 10_1101-2020_10_26_351783 226 10 6 6 CD 10_1101-2020_10_26_351783 226 11 , , , 10_1101-2020_10_26_351783 226 12 2021 2021 CD 10_1101-2020_10_26_351783 226 13 . . . 10_1101-2020_10_26_351783 226 14 ; ; : 10_1101-2020_10_26_351783 226 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 226 16 : : : 10_1101-2020_10_26_351783 226 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 226 18 preprint preprint NN 10_1101-2020_10_26_351783 226 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 226 20 16 16 CD 10_1101-2020_10_26_351783 226 21 signaling signal VBG 10_1101-2020_10_26_351783 226 22 , , , 10_1101-2020_10_26_351783 226 23 Th1 th1 NN 10_1101-2020_10_26_351783 226 24 / / SYM 10_1101-2020_10_26_351783 226 25 Th2 th2 NN 10_1101-2020_10_26_351783 226 26 differentiation differentiation NN 10_1101-2020_10_26_351783 226 27 , , , 10_1101-2020_10_26_351783 226 28 or or CC 10_1101-2020_10_26_351783 226 29 leukocyte leukocyte NN 10_1101-2020_10_26_351783 226 30 transendothelial transendothelial NN 10_1101-2020_10_26_351783 226 31 migration migration NN 10_1101-2020_10_26_351783 226 32 . . . 10_1101-2020_10_26_351783 227 1 These these DT 10_1101-2020_10_26_351783 227 2 results result NNS 10_1101-2020_10_26_351783 227 3 conform conform VBP 10_1101-2020_10_26_351783 227 4 with with IN 10_1101-2020_10_26_351783 227 5 the the DT 10_1101-2020_10_26_351783 227 6 current current JJ 10_1101-2020_10_26_351783 227 7 hypothesis hypothesis NN 10_1101-2020_10_26_351783 227 8 that that WDT 10_1101-2020_10_26_351783 227 9 MS MS NNP 10_1101-2020_10_26_351783 227 10 is be VBZ 10_1101-2020_10_26_351783 227 11 mediated mediate VBN 10_1101-2020_10_26_351783 227 12 by by IN 10_1101-2020_10_26_351783 227 13 an an DT 10_1101-2020_10_26_351783 227 14 autoreactive autoreactive JJ 10_1101-2020_10_26_351783 227 15 response response NN 10_1101-2020_10_26_351783 227 16 of of IN 10_1101-2020_10_26_351783 227 17 CD4 CD4 NNP 10_1101-2020_10_26_351783 227 18 + + SYM 10_1101-2020_10_26_351783 227 19 T t NN 10_1101-2020_10_26_351783 227 20 cells cell NNS 10_1101-2020_10_26_351783 227 21 against against IN 10_1101-2020_10_26_351783 227 22 myelin myelin NNP 10_1101-2020_10_26_351783 227 23 surrounding surround VBG 10_1101-2020_10_26_351783 227 24 neuronal neuronal JJ 10_1101-2020_10_26_351783 227 25 axons axon NNS 10_1101-2020_10_26_351783 227 26 , , , 10_1101-2020_10_26_351783 227 27 preceded precede VBN 10_1101-2020_10_26_351783 227 28 by by IN 10_1101-2020_10_26_351783 227 29 their -PRON- PRP$ 10_1101-2020_10_26_351783 227 30 migration migration NN 10_1101-2020_10_26_351783 227 31 across across IN 10_1101-2020_10_26_351783 227 32 the the DT 10_1101-2020_10_26_351783 227 33 blood blood NN 10_1101-2020_10_26_351783 227 34 - - HYPH 10_1101-2020_10_26_351783 227 35 brain brain NN 10_1101-2020_10_26_351783 227 36 barrier barrier NN 10_1101-2020_10_26_351783 227 37 ( ( -LRB- 10_1101-2020_10_26_351783 227 38 BBB)[37 BBB)[37 NNP 10_1101-2020_10_26_351783 227 39 ] ] -RRB- 10_1101-2020_10_26_351783 227 40 . . . 10_1101-2020_10_26_351783 228 1 This this DT 10_1101-2020_10_26_351783 228 2 autoproliferation autoproliferation NN 10_1101-2020_10_26_351783 228 3 of of IN 10_1101-2020_10_26_351783 228 4 brain brain NN 10_1101-2020_10_26_351783 228 5 - - HYPH 10_1101-2020_10_26_351783 228 6 targeting target VBG 10_1101-2020_10_26_351783 228 7 Th1 th1 NN 10_1101-2020_10_26_351783 228 8 cells cell NNS 10_1101-2020_10_26_351783 228 9 has have VBZ 10_1101-2020_10_26_351783 228 10 been be VBN 10_1101-2020_10_26_351783 228 11 shown show VBN 10_1101-2020_10_26_351783 228 12 to to TO 10_1101-2020_10_26_351783 228 13 be be VB 10_1101-2020_10_26_351783 228 14 driven drive VBN 10_1101-2020_10_26_351783 228 15 by by IN 10_1101-2020_10_26_351783 228 16 memory memory NN 10_1101-2020_10_26_351783 228 17 B b NN 10_1101-2020_10_26_351783 228 18 cells cell NNS 10_1101-2020_10_26_351783 228 19 , , , 10_1101-2020_10_26_351783 228 20 in in IN 10_1101-2020_10_26_351783 228 21 a a DT 10_1101-2020_10_26_351783 228 22 process process NN 10_1101-2020_10_26_351783 228 23 mediated mediate VBN 10_1101-2020_10_26_351783 228 24 by by IN 10_1101-2020_10_26_351783 228 25 HLA HLA NNP 10_1101-2020_10_26_351783 228 26 - - HYPH 10_1101-2020_10_26_351783 228 27 DR15[38 DR15[38 NNP 10_1101-2020_10_26_351783 228 28 ] ] -RRB- 10_1101-2020_10_26_351783 228 29 . . . 10_1101-2020_10_26_351783 229 1 In in IN 10_1101-2020_10_26_351783 229 2 addition addition NN 10_1101-2020_10_26_351783 229 3 , , , 10_1101-2020_10_26_351783 229 4 another another DT 10_1101-2020_10_26_351783 229 5 enriched enriched JJ 10_1101-2020_10_26_351783 229 6 pathway pathway NN 10_1101-2020_10_26_351783 229 7 was be VBD 10_1101-2020_10_26_351783 229 8 VEGF vegf NN 10_1101-2020_10_26_351783 229 9 signaling signal VBG 10_1101-2020_10_26_351783 229 10 . . . 10_1101-2020_10_26_351783 230 1 MS MS NNP 10_1101-2020_10_26_351783 230 2 patients patient NNS 10_1101-2020_10_26_351783 230 3 present present VBP 10_1101-2020_10_26_351783 230 4 high high JJ 10_1101-2020_10_26_351783 230 5 serum serum NN 10_1101-2020_10_26_351783 230 6 VEGF vegf NN 10_1101-2020_10_26_351783 230 7 levels level NNS 10_1101-2020_10_26_351783 230 8 , , , 10_1101-2020_10_26_351783 230 9 which which WDT 10_1101-2020_10_26_351783 230 10 is be VBZ 10_1101-2020_10_26_351783 230 11 related relate VBN 10_1101-2020_10_26_351783 230 12 to to IN 10_1101-2020_10_26_351783 230 13 pro pro JJ 10_1101-2020_10_26_351783 230 14 - - JJ 10_1101-2020_10_26_351783 230 15 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 230 16 functions function NNS 10_1101-2020_10_26_351783 230 17 and and CC 10_1101-2020_10_26_351783 230 18 can can MD 10_1101-2020_10_26_351783 230 19 alter alter VB 10_1101-2020_10_26_351783 230 20 the the DT 10_1101-2020_10_26_351783 230 21 permeability permeability NN 10_1101-2020_10_26_351783 230 22 of of IN 10_1101-2020_10_26_351783 230 23 the the DT 10_1101-2020_10_26_351783 230 24 BBB[39 BBB[39 NNP 10_1101-2020_10_26_351783 230 25 ] ] -RRB- 10_1101-2020_10_26_351783 230 26 . . . 10_1101-2020_10_26_351783 231 1 As as IN 10_1101-2020_10_26_351783 231 2 GWAS GWAS NNP 10_1101-2020_10_26_351783 231 3 was be VBD 10_1101-2020_10_26_351783 231 4 used use VBN 10_1101-2020_10_26_351783 231 5 for for IN 10_1101-2020_10_26_351783 231 6 method method NN 10_1101-2020_10_26_351783 231 7 prioritization prioritization NN 10_1101-2020_10_26_351783 231 8 we -PRON- PRP 10_1101-2020_10_26_351783 231 9 asked ask VBD 10_1101-2020_10_26_351783 231 10 if if IN 10_1101-2020_10_26_351783 231 11 modules module NNS 10_1101-2020_10_26_351783 231 12 instead instead RB 10_1101-2020_10_26_351783 231 13 could could MD 10_1101-2020_10_26_351783 231 14 be be VB 10_1101-2020_10_26_351783 231 15 validated validate VBN 10_1101-2020_10_26_351783 231 16 using use VBG 10_1101-2020_10_26_351783 231 17 epigenetics epigenetic NNS 10_1101-2020_10_26_351783 231 18 and and CC 10_1101-2020_10_26_351783 231 19 lifestyle lifestyle NN 10_1101-2020_10_26_351783 231 20 risk risk NN 10_1101-2020_10_26_351783 231 21 factor factor NN 10_1101-2020_10_26_351783 231 22 genes gene NNS 10_1101-2020_10_26_351783 231 23 that that WDT 10_1101-2020_10_26_351783 231 24 we -PRON- PRP 10_1101-2020_10_26_351783 231 25 identified identify VBD 10_1101-2020_10_26_351783 231 26 to to TO 10_1101-2020_10_26_351783 231 27 associate associate VB 10_1101-2020_10_26_351783 231 28 with with IN 10_1101-2020_10_26_351783 231 29 MS MS NNP 10_1101-2020_10_26_351783 231 30 . . . 10_1101-2020_10_26_351783 231 31 With with IN 10_1101-2020_10_26_351783 231 32 this this DT 10_1101-2020_10_26_351783 231 33 aim aim NN 10_1101-2020_10_26_351783 231 34 , , , 10_1101-2020_10_26_351783 231 35 we -PRON- PRP 10_1101-2020_10_26_351783 231 36 compiled compile VBD 10_1101-2020_10_26_351783 231 37 a a DT 10_1101-2020_10_26_351783 231 38 set set NN 10_1101-2020_10_26_351783 231 39 of of IN 10_1101-2020_10_26_351783 231 40 publicly publicly RB 10_1101-2020_10_26_351783 231 41 available available JJ 10_1101-2020_10_26_351783 231 42 data datum NNS 10_1101-2020_10_26_351783 231 43 from from IN 10_1101-2020_10_26_351783 231 44 omics omic NNS 10_1101-2020_10_26_351783 231 45 studies study NNS 10_1101-2020_10_26_351783 231 46 of of IN 10_1101-2020_10_26_351783 231 47 these these DT 10_1101-2020_10_26_351783 231 48 risk risk NN 10_1101-2020_10_26_351783 231 49 factors factor NNS 10_1101-2020_10_26_351783 231 50 in in IN 10_1101-2020_10_26_351783 231 51 healthy healthy JJ 10_1101-2020_10_26_351783 231 52 individuals individual NNS 10_1101-2020_10_26_351783 231 53 . . . 10_1101-2020_10_26_351783 232 1 This this DT 10_1101-2020_10_26_351783 232 2 analysis analysis NN 10_1101-2020_10_26_351783 232 3 demonstrated demonstrate VBD 10_1101-2020_10_26_351783 232 4 that that IN 10_1101-2020_10_26_351783 232 5 five five CD 10_1101-2020_10_26_351783 232 6 out out IN 10_1101-2020_10_26_351783 232 7 of of IN 10_1101-2020_10_26_351783 232 8 eight eight CD 10_1101-2020_10_26_351783 232 9 risk risk NN 10_1101-2020_10_26_351783 232 10 factors factor NNS 10_1101-2020_10_26_351783 232 11 were be VBD 10_1101-2020_10_26_351783 232 12 enriched enrich VBN 10_1101-2020_10_26_351783 232 13 in in IN 10_1101-2020_10_26_351783 232 14 our -PRON- PRP$ 10_1101-2020_10_26_351783 232 15 module module NN 10_1101-2020_10_26_351783 232 16 . . . 10_1101-2020_10_26_351783 233 1 In in IN 10_1101-2020_10_26_351783 233 2 order order NN 10_1101-2020_10_26_351783 233 3 to to TO 10_1101-2020_10_26_351783 233 4 validate validate VB 10_1101-2020_10_26_351783 233 5 the the DT 10_1101-2020_10_26_351783 233 6 use use NN 10_1101-2020_10_26_351783 233 7 of of IN 10_1101-2020_10_26_351783 233 8 an an DT 10_1101-2020_10_26_351783 233 9 environmental environmental JJ 10_1101-2020_10_26_351783 233 10 assessment assessment NN 10_1101-2020_10_26_351783 233 11 using use VBG 10_1101-2020_10_26_351783 233 12 public public JJ 10_1101-2020_10_26_351783 233 13 domain domain NN 10_1101-2020_10_26_351783 233 14 risk risk NN 10_1101-2020_10_26_351783 233 15 factor factor NN 10_1101-2020_10_26_351783 233 16 association association NNP 10_1101-2020_10_26_351783 233 17 we -PRON- PRP 10_1101-2020_10_26_351783 233 18 found find VBD 10_1101-2020_10_26_351783 233 19 an an DT 10_1101-2020_10_26_351783 233 20 independent independent JJ 10_1101-2020_10_26_351783 233 21 methylome methylome JJ 10_1101-2020_10_26_351783 233 22 study study NN 10_1101-2020_10_26_351783 233 23 of of IN 10_1101-2020_10_26_351783 233 24 MS MS NNP 10_1101-2020_10_26_351783 233 25 comprising comprise VBG 10_1101-2020_10_26_351783 233 26 environmental environmental JJ 10_1101-2020_10_26_351783 233 27 data datum NNS 10_1101-2020_10_26_351783 233 28 for for IN 10_1101-2020_10_26_351783 233 29 each each DT 10_1101-2020_10_26_351783 233 30 MS MS NNP 10_1101-2020_10_26_351783 233 31 and and CC 10_1101-2020_10_26_351783 233 32 healthy healthy JJ 10_1101-2020_10_26_351783 233 33 individual individual NN 10_1101-2020_10_26_351783 233 34 . . . 10_1101-2020_10_26_351783 234 1 This this DT 10_1101-2020_10_26_351783 234 2 analysis analysis NN 10_1101-2020_10_26_351783 234 3 showed show VBD 10_1101-2020_10_26_351783 234 4 a a DT 10_1101-2020_10_26_351783 234 5 remarkable remarkable JJ 10_1101-2020_10_26_351783 234 6 enrichment enrichment NN 10_1101-2020_10_26_351783 234 7 of of IN 10_1101-2020_10_26_351783 234 8 the the DT 10_1101-2020_10_26_351783 234 9 220 220 CD 10_1101-2020_10_26_351783 234 10 module module JJ 10_1101-2020_10_26_351783 234 11 genes gene NNS 10_1101-2020_10_26_351783 234 12 by by IN 10_1101-2020_10_26_351783 234 13 217 217 CD 10_1101-2020_10_26_351783 234 14 to to TO 10_1101-2020_10_26_351783 234 15 differentially differentially RB 10_1101-2020_10_26_351783 234 16 methylated methylate VBN 10_1101-2020_10_26_351783 234 17 genes gene NNS 10_1101-2020_10_26_351783 234 18 for for IN 10_1101-2020_10_26_351783 234 19 MS MS NNP 10_1101-2020_10_26_351783 234 20 ( ( -LRB- 10_1101-2020_10_26_351783 234 21 P p NN 10_1101-2020_10_26_351783 234 22 = = SYM 10_1101-2020_10_26_351783 234 23 1.2 1.2 CD 10_1101-2020_10_26_351783 234 24 x x SYM 10_1101-2020_10_26_351783 234 25 10 10 CD 10_1101-2020_10_26_351783 234 26 - - SYM 10_1101-2020_10_26_351783 234 27 47 47 CD 10_1101-2020_10_26_351783 234 28 ) ) -RRB- 10_1101-2020_10_26_351783 234 29 , , , 10_1101-2020_10_26_351783 234 30 and and CC 10_1101-2020_10_26_351783 234 31 a a DT 10_1101-2020_10_26_351783 234 32 majority majority NN 10_1101-2020_10_26_351783 234 33 to to TO 10_1101-2020_10_26_351783 234 34 be be VB 10_1101-2020_10_26_351783 234 35 associated associate VBN 10_1101-2020_10_26_351783 234 36 with with IN 10_1101-2020_10_26_351783 234 37 the the DT 10_1101-2020_10_26_351783 234 38 tested test VBN 10_1101-2020_10_26_351783 234 39 risk risk NN 10_1101-2020_10_26_351783 234 40 factors factor NNS 10_1101-2020_10_26_351783 234 41 . . . 10_1101-2020_10_26_351783 235 1 In in IN 10_1101-2020_10_26_351783 235 2 contrast contrast NN 10_1101-2020_10_26_351783 235 3 to to TO 10_1101-2020_10_26_351783 235 4 previously previously RB 10_1101-2020_10_26_351783 235 5 known know VBN 10_1101-2020_10_26_351783 235 6 community community NN 10_1101-2020_10_26_351783 235 7 challenges challenge NNS 10_1101-2020_10_26_351783 235 8 , , , 10_1101-2020_10_26_351783 235 9 in in IN 10_1101-2020_10_26_351783 235 10 our -PRON- PRP$ 10_1101-2020_10_26_351783 235 11 study study NN 10_1101-2020_10_26_351783 235 12 we -PRON- PRP 10_1101-2020_10_26_351783 235 13 not not RB 10_1101-2020_10_26_351783 235 14 only only RB 10_1101-2020_10_26_351783 235 15 used use VBD 10_1101-2020_10_26_351783 235 16 the the DT 10_1101-2020_10_26_351783 235 17 topological topological JJ 10_1101-2020_10_26_351783 235 18 property property NN 10_1101-2020_10_26_351783 235 19 of of IN 10_1101-2020_10_26_351783 235 20 the the DT 10_1101-2020_10_26_351783 235 21 network network NN 10_1101-2020_10_26_351783 235 22 , , , 10_1101-2020_10_26_351783 235 23 but but CC 10_1101-2020_10_26_351783 235 24 we -PRON- PRP 10_1101-2020_10_26_351783 235 25 also also RB 10_1101-2020_10_26_351783 235 26 combined combine VBD 10_1101-2020_10_26_351783 235 27 the the DT 10_1101-2020_10_26_351783 235 28 methods method NNS 10_1101-2020_10_26_351783 235 29 to to TO 10_1101-2020_10_26_351783 235 30 use use VB 10_1101-2020_10_26_351783 235 31 an an DT 10_1101-2020_10_26_351783 235 32 omics omic NNS 10_1101-2020_10_26_351783 235 33 - - HYPH 10_1101-2020_10_26_351783 235 34 based base VBN 10_1101-2020_10_26_351783 235 35 input input NN 10_1101-2020_10_26_351783 235 36 to to TO 10_1101-2020_10_26_351783 235 37 uncover uncover VB 10_1101-2020_10_26_351783 235 38 the the DT 10_1101-2020_10_26_351783 235 39 disease disease NN 10_1101-2020_10_26_351783 235 40 modules module NNS 10_1101-2020_10_26_351783 235 41 that that WDT 10_1101-2020_10_26_351783 235 42 might may MD 10_1101-2020_10_26_351783 235 43 be be VB 10_1101-2020_10_26_351783 235 44 dysregulated dysregulate VBN 10_1101-2020_10_26_351783 235 45 at at IN 10_1101-2020_10_26_351783 235 46 each each DT 10_1101-2020_10_26_351783 235 47 omics omic NNS 10_1101-2020_10_26_351783 235 48 level level NN 10_1101-2020_10_26_351783 235 49 , , , 10_1101-2020_10_26_351783 235 50 contributing contribute VBG 10_1101-2020_10_26_351783 235 51 to to IN 10_1101-2020_10_26_351783 235 52 the the DT 10_1101-2020_10_26_351783 235 53 diverse diverse JJ 10_1101-2020_10_26_351783 235 54 causative causative JJ 10_1101-2020_10_26_351783 235 55 mechanisms mechanism NNS 10_1101-2020_10_26_351783 235 56 behind behind IN 10_1101-2020_10_26_351783 235 57 complex complex JJ 10_1101-2020_10_26_351783 235 58 diseases disease NNS 10_1101-2020_10_26_351783 235 59 . . . 10_1101-2020_10_26_351783 236 1 Although although IN 10_1101-2020_10_26_351783 236 2 using use VBG 10_1101-2020_10_26_351783 236 3 the the DT 10_1101-2020_10_26_351783 236 4 PPI PPI NNP 10_1101-2020_10_26_351783 236 5 network network NN 10_1101-2020_10_26_351783 236 6 as as IN 10_1101-2020_10_26_351783 236 7 background background NN 10_1101-2020_10_26_351783 236 8 may may MD 10_1101-2020_10_26_351783 236 9 lead lead VB 10_1101-2020_10_26_351783 236 10 to to IN 10_1101-2020_10_26_351783 236 11 certain certain JJ 10_1101-2020_10_26_351783 236 12 knowledge knowledge NN 10_1101-2020_10_26_351783 236 13 bias bias NN 10_1101-2020_10_26_351783 236 14 , , , 10_1101-2020_10_26_351783 236 15 this this DT 10_1101-2020_10_26_351783 236 16 kind kind NN 10_1101-2020_10_26_351783 236 17 of of IN 10_1101-2020_10_26_351783 236 18 benchmark benchmark NN 10_1101-2020_10_26_351783 236 19 allowed allow VBD 10_1101-2020_10_26_351783 236 20 us -PRON- PRP 10_1101-2020_10_26_351783 236 21 to to TO 10_1101-2020_10_26_351783 236 22 look look VB 10_1101-2020_10_26_351783 236 23 at at IN 10_1101-2020_10_26_351783 236 24 the the DT 10_1101-2020_10_26_351783 236 25 relevant relevant JJ 10_1101-2020_10_26_351783 236 26 risk risk NN 10_1101-2020_10_26_351783 236 27 factors factor NNS 10_1101-2020_10_26_351783 236 28 . . . 10_1101-2020_10_26_351783 237 1 In in IN 10_1101-2020_10_26_351783 237 2 our -PRON- PRP$ 10_1101-2020_10_26_351783 237 3 assessment assessment NN 10_1101-2020_10_26_351783 237 4 of of IN 10_1101-2020_10_26_351783 237 5 the the DT 10_1101-2020_10_26_351783 237 6 disease disease NN 10_1101-2020_10_26_351783 237 7 modules module NNS 10_1101-2020_10_26_351783 237 8 , , , 10_1101-2020_10_26_351783 237 9 methods method NNS 10_1101-2020_10_26_351783 237 10 such such JJ 10_1101-2020_10_26_351783 237 11 as as IN 10_1101-2020_10_26_351783 237 12 Clique Clique NNP 10_1101-2020_10_26_351783 237 13 SuM sum NN 10_1101-2020_10_26_351783 237 14 and and CC 10_1101-2020_10_26_351783 237 15 DIAMOnD diamond NN 10_1101-2020_10_26_351783 237 16 did do VBD 10_1101-2020_10_26_351783 237 17 perform perform VB 10_1101-2020_10_26_351783 237 18 better well RBR 10_1101-2020_10_26_351783 237 19 than than IN 10_1101-2020_10_26_351783 237 20 the the DT 10_1101-2020_10_26_351783 237 21 community community NN 10_1101-2020_10_26_351783 237 22 - - HYPH 10_1101-2020_10_26_351783 237 23 based base VBN 10_1101-2020_10_26_351783 237 24 consensus consensus NN 10_1101-2020_10_26_351783 237 25 predictions prediction NNS 10_1101-2020_10_26_351783 237 26 . . . 10_1101-2020_10_26_351783 238 1 In in IN 10_1101-2020_10_26_351783 238 2 summary summary NN 10_1101-2020_10_26_351783 238 3 , , , 10_1101-2020_10_26_351783 238 4 our -PRON- PRP$ 10_1101-2020_10_26_351783 238 5 study study NN 10_1101-2020_10_26_351783 238 6 provides provide VBZ 10_1101-2020_10_26_351783 238 7 a a DT 10_1101-2020_10_26_351783 238 8 practical practical JJ 10_1101-2020_10_26_351783 238 9 integrative integrative JJ 10_1101-2020_10_26_351783 238 10 workflow workflow NN 10_1101-2020_10_26_351783 238 11 that that WDT 10_1101-2020_10_26_351783 238 12 enables enable VBZ 10_1101-2020_10_26_351783 238 13 system system NN 10_1101-2020_10_26_351783 238 14 - - HYPH 10_1101-2020_10_26_351783 238 15 level level NN 10_1101-2020_10_26_351783 238 16 analysis analysis NN 10_1101-2020_10_26_351783 238 17 of of IN 10_1101-2020_10_26_351783 238 18 heterogeneous heterogeneous JJ 10_1101-2020_10_26_351783 238 19 diseases disease NNS 10_1101-2020_10_26_351783 238 20 , , , 10_1101-2020_10_26_351783 238 21 in in IN 10_1101-2020_10_26_351783 238 22 terms term NNS 10_1101-2020_10_26_351783 238 23 of of IN 10_1101-2020_10_26_351783 238 24 multi multi JJ 10_1101-2020_10_26_351783 238 25 - - HYPH 10_1101-2020_10_26_351783 238 26 omics omics NNP 10_1101-2020_10_26_351783 238 27 disease disease NN 10_1101-2020_10_26_351783 238 28 modules module NNS 10_1101-2020_10_26_351783 238 29 , , , 10_1101-2020_10_26_351783 238 30 as as RB 10_1101-2020_10_26_351783 238 31 well well RB 10_1101-2020_10_26_351783 238 32 as as IN 10_1101-2020_10_26_351783 238 33 the the DT 10_1101-2020_10_26_351783 238 34 validation validation NN 10_1101-2020_10_26_351783 238 35 of of IN 10_1101-2020_10_26_351783 238 36 these these DT 10_1101-2020_10_26_351783 238 37 by by IN 10_1101-2020_10_26_351783 238 38 using use VBG 10_1101-2020_10_26_351783 238 39 both both DT 10_1101-2020_10_26_351783 238 40 disease disease NN 10_1101-2020_10_26_351783 238 41 - - HYPH 10_1101-2020_10_26_351783 238 42 specific specific JJ 10_1101-2020_10_26_351783 238 43 GWAS gwas NN 10_1101-2020_10_26_351783 238 44 and and CC 10_1101-2020_10_26_351783 238 45 risk risk NN 10_1101-2020_10_26_351783 238 46 factors factor NNS 10_1101-2020_10_26_351783 238 47 enrichment enrichment NN 10_1101-2020_10_26_351783 238 48 . . . 10_1101-2020_10_26_351783 239 1 We -PRON- PRP 10_1101-2020_10_26_351783 239 2 believe believe VBP 10_1101-2020_10_26_351783 239 3 that that IN 10_1101-2020_10_26_351783 239 4 this this DT 10_1101-2020_10_26_351783 239 5 analysis analysis NN 10_1101-2020_10_26_351783 239 6 ( ( -LRB- 10_1101-2020_10_26_351783 239 7 which which WDT 10_1101-2020_10_26_351783 239 8 was be VBD 10_1101-2020_10_26_351783 239 9 not not RB 10_1101-2020_10_26_351783 239 10 certified certify VBN 10_1101-2020_10_26_351783 239 11 by by IN 10_1101-2020_10_26_351783 239 12 peer peer NN 10_1101-2020_10_26_351783 239 13 review review NN 10_1101-2020_10_26_351783 239 14 ) ) -RRB- 10_1101-2020_10_26_351783 239 15 is be VBZ 10_1101-2020_10_26_351783 239 16 the the DT 10_1101-2020_10_26_351783 239 17 author author NN 10_1101-2020_10_26_351783 239 18 / / SYM 10_1101-2020_10_26_351783 239 19 funder funder NN 10_1101-2020_10_26_351783 239 20 . . . 10_1101-2020_10_26_351783 240 1 All all DT 10_1101-2020_10_26_351783 240 2 rights right NNS 10_1101-2020_10_26_351783 240 3 reserved reserve VBD 10_1101-2020_10_26_351783 240 4 . . . 10_1101-2020_10_26_351783 241 1 No no DT 10_1101-2020_10_26_351783 241 2 reuse reuse NN 10_1101-2020_10_26_351783 241 3 allowed allow VBN 10_1101-2020_10_26_351783 241 4 without without IN 10_1101-2020_10_26_351783 241 5 permission permission NN 10_1101-2020_10_26_351783 241 6 . . . 10_1101-2020_10_26_351783 242 1 The the DT 10_1101-2020_10_26_351783 242 2 copyright copyright NN 10_1101-2020_10_26_351783 242 3 holder holder NN 10_1101-2020_10_26_351783 242 4 for for IN 10_1101-2020_10_26_351783 242 5 this this DT 10_1101-2020_10_26_351783 242 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 242 7 version version NN 10_1101-2020_10_26_351783 242 8 posted post VBD 10_1101-2020_10_26_351783 242 9 January January NNP 10_1101-2020_10_26_351783 242 10 6 6 CD 10_1101-2020_10_26_351783 242 11 , , , 10_1101-2020_10_26_351783 242 12 2021 2021 CD 10_1101-2020_10_26_351783 242 13 . . . 10_1101-2020_10_26_351783 242 14 ; ; : 10_1101-2020_10_26_351783 242 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 242 16 : : : 10_1101-2020_10_26_351783 242 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 242 18 preprint preprint NN 10_1101-2020_10_26_351783 242 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 242 20 17 17 CD 10_1101-2020_10_26_351783 242 21 validates validate NNS 10_1101-2020_10_26_351783 242 22 our -PRON- PRP$ 10_1101-2020_10_26_351783 242 23 integrated integrated JJ 10_1101-2020_10_26_351783 242 24 use use NN 10_1101-2020_10_26_351783 242 25 datasets dataset NNS 10_1101-2020_10_26_351783 242 26 and and CC 10_1101-2020_10_26_351783 242 27 suggest suggest VBP 10_1101-2020_10_26_351783 242 28 a a DT 10_1101-2020_10_26_351783 242 29 pipeline pipeline NN 10_1101-2020_10_26_351783 242 30 that that WDT 10_1101-2020_10_26_351783 242 31 readily readily RB 10_1101-2020_10_26_351783 242 32 could could MD 10_1101-2020_10_26_351783 242 33 be be VB 10_1101-2020_10_26_351783 242 34 tested test VBN 10_1101-2020_10_26_351783 242 35 in in RP 10_1101-2020_10_26_351783 242 36 at at RB 10_1101-2020_10_26_351783 242 37 least least JJS 10_1101-2020_10_26_351783 242 38 in in IN 10_1101-2020_10_26_351783 242 39 other other JJ 10_1101-2020_10_26_351783 242 40 autoimmune autoimmune JJ 10_1101-2020_10_26_351783 242 41 and and CC 10_1101-2020_10_26_351783 242 42 cardiovascular cardiovascular JJ 10_1101-2020_10_26_351783 242 43 diseases disease NNS 10_1101-2020_10_26_351783 242 44 . . . 10_1101-2020_10_26_351783 243 1 Lastly lastly RB 10_1101-2020_10_26_351783 243 2 , , , 10_1101-2020_10_26_351783 243 3 our -PRON- PRP$ 10_1101-2020_10_26_351783 243 4 study study NN 10_1101-2020_10_26_351783 243 5 did do VBD 10_1101-2020_10_26_351783 243 6 not not RB 10_1101-2020_10_26_351783 243 7 aim aim VB 10_1101-2020_10_26_351783 243 8 to to TO 10_1101-2020_10_26_351783 243 9 optimize optimize VB 10_1101-2020_10_26_351783 243 10 hyper- hyper- JJ 10_1101-2020_10_26_351783 243 11 parameters parameter NNS 10_1101-2020_10_26_351783 243 12 for for IN 10_1101-2020_10_26_351783 243 13 individual individual JJ 10_1101-2020_10_26_351783 243 14 disease disease NN 10_1101-2020_10_26_351783 243 15 modules module NNS 10_1101-2020_10_26_351783 243 16 , , , 10_1101-2020_10_26_351783 243 17 and and CC 10_1101-2020_10_26_351783 243 18 instead instead RB 10_1101-2020_10_26_351783 243 19 used use VBD 10_1101-2020_10_26_351783 243 20 default default NN 10_1101-2020_10_26_351783 243 21 values value NNS 10_1101-2020_10_26_351783 243 22 when when WRB 10_1101-2020_10_26_351783 243 23 possible possible JJ 10_1101-2020_10_26_351783 243 24 , , , 10_1101-2020_10_26_351783 243 25 and and CC 10_1101-2020_10_26_351783 243 26 to to IN 10_1101-2020_10_26_351783 243 27 the the DT 10_1101-2020_10_26_351783 243 28 methods method NNS 10_1101-2020_10_26_351783 243 29 from from IN 10_1101-2020_10_26_351783 243 30 the the DT 10_1101-2020_10_26_351783 243 31 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 243 32 R r NN 10_1101-2020_10_26_351783 243 33 package package NN 10_1101-2020_10_26_351783 243 34 implementation implementation NN 10_1101-2020_10_26_351783 243 35 of of IN 10_1101-2020_10_26_351783 243 36 the the DT 10_1101-2020_10_26_351783 243 37 methods[13 methods[13 NNP 10_1101-2020_10_26_351783 243 38 ] ] -RRB- 10_1101-2020_10_26_351783 243 39 . . . 10_1101-2020_10_26_351783 244 1 However however RB 10_1101-2020_10_26_351783 244 2 , , , 10_1101-2020_10_26_351783 244 3 this this DT 10_1101-2020_10_26_351783 244 4 might may MD 10_1101-2020_10_26_351783 244 5 be be VB 10_1101-2020_10_26_351783 244 6 an an DT 10_1101-2020_10_26_351783 244 7 important important JJ 10_1101-2020_10_26_351783 244 8 task task NN 10_1101-2020_10_26_351783 244 9 for for IN 10_1101-2020_10_26_351783 244 10 specific specific JJ 10_1101-2020_10_26_351783 244 11 disease disease NN 10_1101-2020_10_26_351783 244 12 and and CC 10_1101-2020_10_26_351783 244 13 our -PRON- PRP$ 10_1101-2020_10_26_351783 244 14 code code NN 10_1101-2020_10_26_351783 244 15 and and CC 10_1101-2020_10_26_351783 244 16 processed process VBN 10_1101-2020_10_26_351783 244 17 datasets dataset NNS 10_1101-2020_10_26_351783 244 18 are be VBP 10_1101-2020_10_26_351783 244 19 available available JJ 10_1101-2020_10_26_351783 244 20 at at IN 10_1101-2020_10_26_351783 244 21 GitLab GitLab NNP 10_1101-2020_10_26_351783 244 22 ( ( -LRB- 10_1101-2020_10_26_351783 244 23 https://gitlab.com/Gustafsson-lab/modifier-benchmark https://gitlab.com/Gustafsson-lab/modifier-benchmark NNP 10_1101-2020_10_26_351783 244 24 ) ) -RRB- 10_1101-2020_10_26_351783 244 25 . . . 10_1101-2020_10_26_351783 245 1 In in IN 10_1101-2020_10_26_351783 245 2 future future JJ 10_1101-2020_10_26_351783 245 3 work work NN 10_1101-2020_10_26_351783 245 4 , , , 10_1101-2020_10_26_351783 245 5 this this DT 10_1101-2020_10_26_351783 245 6 approach approach NN 10_1101-2020_10_26_351783 245 7 can can MD 10_1101-2020_10_26_351783 245 8 be be VB 10_1101-2020_10_26_351783 245 9 expanded expand VBN 10_1101-2020_10_26_351783 245 10 to to TO 10_1101-2020_10_26_351783 245 11 include include VB 10_1101-2020_10_26_351783 245 12 diverse diverse JJ 10_1101-2020_10_26_351783 245 13 and and CC 10_1101-2020_10_26_351783 245 14 context context NN 10_1101-2020_10_26_351783 245 15 - - HYPH 10_1101-2020_10_26_351783 245 16 specific specific JJ 10_1101-2020_10_26_351783 245 17 networks network NNS 10_1101-2020_10_26_351783 245 18 to to TO 10_1101-2020_10_26_351783 245 19 determine determine VB 10_1101-2020_10_26_351783 245 20 whether whether IN 10_1101-2020_10_26_351783 245 21 our -PRON- PRP$ 10_1101-2020_10_26_351783 245 22 multi multi JJ 10_1101-2020_10_26_351783 245 23 - - NNS 10_1101-2020_10_26_351783 245 24 omics omics JJ 10_1101-2020_10_26_351783 245 25 modules module NNS 10_1101-2020_10_26_351783 245 26 are be VBP 10_1101-2020_10_26_351783 245 27 able able JJ 10_1101-2020_10_26_351783 245 28 to to TO 10_1101-2020_10_26_351783 245 29 capture capture VB 10_1101-2020_10_26_351783 245 30 various various JJ 10_1101-2020_10_26_351783 245 31 other other JJ 10_1101-2020_10_26_351783 245 32 levels level NNS 10_1101-2020_10_26_351783 245 33 of of IN 10_1101-2020_10_26_351783 245 34 granularity granularity NN 10_1101-2020_10_26_351783 245 35 . . . 10_1101-2020_10_26_351783 246 1 ( ( -LRB- 10_1101-2020_10_26_351783 246 2 which which WDT 10_1101-2020_10_26_351783 246 3 was be VBD 10_1101-2020_10_26_351783 246 4 not not RB 10_1101-2020_10_26_351783 246 5 certified certify VBN 10_1101-2020_10_26_351783 246 6 by by IN 10_1101-2020_10_26_351783 246 7 peer peer NN 10_1101-2020_10_26_351783 246 8 review review NN 10_1101-2020_10_26_351783 246 9 ) ) -RRB- 10_1101-2020_10_26_351783 246 10 is be VBZ 10_1101-2020_10_26_351783 246 11 the the DT 10_1101-2020_10_26_351783 246 12 author author NN 10_1101-2020_10_26_351783 246 13 / / SYM 10_1101-2020_10_26_351783 246 14 funder funder NN 10_1101-2020_10_26_351783 246 15 . . . 10_1101-2020_10_26_351783 247 1 All all DT 10_1101-2020_10_26_351783 247 2 rights right NNS 10_1101-2020_10_26_351783 247 3 reserved reserve VBD 10_1101-2020_10_26_351783 247 4 . . . 10_1101-2020_10_26_351783 248 1 No no DT 10_1101-2020_10_26_351783 248 2 reuse reuse NN 10_1101-2020_10_26_351783 248 3 allowed allow VBN 10_1101-2020_10_26_351783 248 4 without without IN 10_1101-2020_10_26_351783 248 5 permission permission NN 10_1101-2020_10_26_351783 248 6 . . . 10_1101-2020_10_26_351783 249 1 The the DT 10_1101-2020_10_26_351783 249 2 copyright copyright NN 10_1101-2020_10_26_351783 249 3 holder holder NN 10_1101-2020_10_26_351783 249 4 for for IN 10_1101-2020_10_26_351783 249 5 this this DT 10_1101-2020_10_26_351783 249 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 249 7 version version NN 10_1101-2020_10_26_351783 249 8 posted post VBD 10_1101-2020_10_26_351783 249 9 January January NNP 10_1101-2020_10_26_351783 249 10 6 6 CD 10_1101-2020_10_26_351783 249 11 , , , 10_1101-2020_10_26_351783 249 12 2021 2021 CD 10_1101-2020_10_26_351783 249 13 . . . 10_1101-2020_10_26_351783 249 14 ; ; : 10_1101-2020_10_26_351783 249 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 249 16 : : : 10_1101-2020_10_26_351783 249 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 249 18 preprint preprint NN 10_1101-2020_10_26_351783 249 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 249 20 18 18 CD 10_1101-2020_10_26_351783 249 21 DECLARATIONS declaration NNS 10_1101-2020_10_26_351783 249 22 ETHICS ethic NNS 10_1101-2020_10_26_351783 249 23 APPROVAL APPROVAL NNS 10_1101-2020_10_26_351783 249 24 AND and CC 10_1101-2020_10_26_351783 249 25 CONSENT consent VBP 10_1101-2020_10_26_351783 249 26 TO to TO 10_1101-2020_10_26_351783 249 27 PARTICIPATE PARTICIPATE NNP 10_1101-2020_10_26_351783 249 28 Not not RB 10_1101-2020_10_26_351783 249 29 applicable applicable JJ 10_1101-2020_10_26_351783 249 30 AVAILABILITY AVAILABILITY NNS 10_1101-2020_10_26_351783 249 31 OF of IN 10_1101-2020_10_26_351783 249 32 DATA datum NNS 10_1101-2020_10_26_351783 249 33 AND and CC 10_1101-2020_10_26_351783 249 34 MATERIALS material NNS 10_1101-2020_10_26_351783 249 35 The the DT 10_1101-2020_10_26_351783 249 36 data datum NNS 10_1101-2020_10_26_351783 249 37 used use VBN 10_1101-2020_10_26_351783 249 38 for for IN 10_1101-2020_10_26_351783 249 39 transcriptomic transcriptomic NNP 10_1101-2020_10_26_351783 249 40 benchmark benchmark NN 10_1101-2020_10_26_351783 249 41 and and CC 10_1101-2020_10_26_351783 249 42 methylation methylation NN 10_1101-2020_10_26_351783 249 43 benchmark benchmark NN 10_1101-2020_10_26_351783 249 44 are be VBP 10_1101-2020_10_26_351783 249 45 downloaded download VBN 10_1101-2020_10_26_351783 249 46 from from IN 10_1101-2020_10_26_351783 249 47 GEO GEO NNP 10_1101-2020_10_26_351783 249 48 . . . 10_1101-2020_10_26_351783 250 1 The the DT 10_1101-2020_10_26_351783 250 2 disease disease NN 10_1101-2020_10_26_351783 250 3 specific specific JJ 10_1101-2020_10_26_351783 250 4 GWAS GWAS NNP 10_1101-2020_10_26_351783 250 5 files file NNS 10_1101-2020_10_26_351783 250 6 are be VBP 10_1101-2020_10_26_351783 250 7 downloaded download VBN 10_1101-2020_10_26_351783 250 8 from from IN 10_1101-2020_10_26_351783 250 9 the the DT 10_1101-2020_10_26_351783 250 10 latest late JJS 10_1101-2020_10_26_351783 250 11 Pascal pascal JJ 10_1101-2020_10_26_351783 250 12 version version NN 10_1101-2020_10_26_351783 250 13 . . . 10_1101-2020_10_26_351783 251 1 The the DT 10_1101-2020_10_26_351783 251 2 processed process VBN 10_1101-2020_10_26_351783 251 3 Data Data NNP 10_1101-2020_10_26_351783 251 4 for for IN 10_1101-2020_10_26_351783 251 5 analysis analysis NN 10_1101-2020_10_26_351783 251 6 is be VBZ 10_1101-2020_10_26_351783 251 7 available available JJ 10_1101-2020_10_26_351783 251 8 at at IN 10_1101-2020_10_26_351783 251 9 https://gitlab.com/Gustafsson-lab/modifier-benchmark.The https://gitlab.com/gustafsson-lab/modifier-benchmark.the CD 10_1101-2020_10_26_351783 251 10 risk risk NN 10_1101-2020_10_26_351783 251 11 factor factor NN 10_1101-2020_10_26_351783 251 12 ( ( -LRB- 10_1101-2020_10_26_351783 251 13 EIMS eims NN 10_1101-2020_10_26_351783 251 14 ) ) -RRB- 10_1101-2020_10_26_351783 251 15 data datum NNS 10_1101-2020_10_26_351783 251 16 will will MD 10_1101-2020_10_26_351783 251 17 be be VB 10_1101-2020_10_26_351783 251 18 made make VBN 10_1101-2020_10_26_351783 251 19 available available JJ 10_1101-2020_10_26_351783 251 20 on on IN 10_1101-2020_10_26_351783 251 21 request request NN 10_1101-2020_10_26_351783 251 22 . . . 10_1101-2020_10_26_351783 252 1 The the DT 10_1101-2020_10_26_351783 252 2 R r NN 10_1101-2020_10_26_351783 252 3 - - HYPH 10_1101-2020_10_26_351783 252 4 package package NN 10_1101-2020_10_26_351783 252 5 MODifieR modifier NN 10_1101-2020_10_26_351783 252 6 is be VBZ 10_1101-2020_10_26_351783 252 7 available available JJ 10_1101-2020_10_26_351783 252 8 on on IN 10_1101-2020_10_26_351783 252 9 the the DT 10_1101-2020_10_26_351783 252 10 GitLab GitLab NNP 10_1101-2020_10_26_351783 252 11 : : : 10_1101-2020_10_26_351783 252 12 https://gitlab.com/Gustafsson-lab/MODifieR https://gitlab.com/Gustafsson-lab/MODifieR NNP 10_1101-2020_10_26_351783 252 13 ; ; : 10_1101-2020_10_26_351783 252 14 the the DT 10_1101-2020_10_26_351783 252 15 code code NN 10_1101-2020_10_26_351783 252 16 used use VBN 10_1101-2020_10_26_351783 252 17 for for IN 10_1101-2020_10_26_351783 252 18 benchmark benchmark JJ 10_1101-2020_10_26_351783 252 19 analysis analysis NN 10_1101-2020_10_26_351783 252 20 and and CC 10_1101-2020_10_26_351783 252 21 risk risk NN 10_1101-2020_10_26_351783 252 22 factor factor NN 10_1101-2020_10_26_351783 252 23 analysis analysis NN 10_1101-2020_10_26_351783 252 24 is be VBZ 10_1101-2020_10_26_351783 252 25 available available JJ 10_1101-2020_10_26_351783 252 26 on on IN 10_1101-2020_10_26_351783 252 27 GitLab GitLab NNP 10_1101-2020_10_26_351783 252 28 : : : 10_1101-2020_10_26_351783 252 29 https://gitlab.com/Gustafsson-lab/modifier-benchmark https://gitlab.com/gustafsson-lab/modifier-benchmark NN 10_1101-2020_10_26_351783 252 30 ; ; : 10_1101-2020_10_26_351783 252 31 the the DT 10_1101-2020_10_26_351783 252 32 latest late JJS 10_1101-2020_10_26_351783 252 33 Pascal pascal JJ 10_1101-2020_10_26_351783 252 34 version version NN 10_1101-2020_10_26_351783 252 35 : : : 10_1101-2020_10_26_351783 252 36 https://www2.unil.ch/cbg/index.php?title=Pascal https://www2.unil.ch/cbg/index.php?title=pascal JJ 10_1101-2020_10_26_351783 252 37 . . . 10_1101-2020_10_26_351783 253 1 COMPETING compete VBG 10_1101-2020_10_26_351783 253 2 INTERESTS INTERESTS NNP 10_1101-2020_10_26_351783 253 3 The the DT 10_1101-2020_10_26_351783 253 4 authors author NNS 10_1101-2020_10_26_351783 253 5 declare declare VBP 10_1101-2020_10_26_351783 253 6 no no DT 10_1101-2020_10_26_351783 253 7 competing compete VBG 10_1101-2020_10_26_351783 253 8 interests interest NNS 10_1101-2020_10_26_351783 253 9 . . . 10_1101-2020_10_26_351783 254 1 FUNDING fund VBG 10_1101-2020_10_26_351783 254 2 This this DT 10_1101-2020_10_26_351783 254 3 work work NN 10_1101-2020_10_26_351783 254 4 was be VBD 10_1101-2020_10_26_351783 254 5 supported support VBN 10_1101-2020_10_26_351783 254 6 by by IN 10_1101-2020_10_26_351783 254 7 the the DT 10_1101-2020_10_26_351783 254 8 Swedish Swedish NNP 10_1101-2020_10_26_351783 254 9 Research Research NNP 10_1101-2020_10_26_351783 254 10 Council Council NNP 10_1101-2020_10_26_351783 254 11 ( ( -LRB- 10_1101-2020_10_26_351783 254 12 grant grant NNP 10_1101-2020_10_26_351783 254 13 2015 2015 CD 10_1101-2020_10_26_351783 254 14 - - HYPH 10_1101-2020_10_26_351783 254 15 03807(M.G. 03807(m.g. CD 10_1101-2020_10_26_351783 255 1 ) ) -RRB- 10_1101-2020_10_26_351783 255 2 , , , 10_1101-2020_10_26_351783 255 3 grant grant VB 10_1101-2020_10_26_351783 255 4 2018- 2018- CD 10_1101-2020_10_26_351783 255 5 02638(M.J. 02638(m.j. CD 10_1101-2020_10_26_351783 255 6 ) ) -RRB- 10_1101-2020_10_26_351783 255 7 ) ) -RRB- 10_1101-2020_10_26_351783 255 8 , , , 10_1101-2020_10_26_351783 255 9 the the DT 10_1101-2020_10_26_351783 255 10 Swedish swedish JJ 10_1101-2020_10_26_351783 255 11 foundation foundation NN 10_1101-2020_10_26_351783 255 12 for for IN 10_1101-2020_10_26_351783 255 13 strategic strategic JJ 10_1101-2020_10_26_351783 255 14 research research NN 10_1101-2020_10_26_351783 255 15 ( ( -LRB- 10_1101-2020_10_26_351783 255 16 grant grant VB 10_1101-2020_10_26_351783 255 17 SB16 SB16 NNP 10_1101-2020_10_26_351783 255 18 - - HYPH 10_1101-2020_10_26_351783 255 19 0095(M.G. 0095(M.G. NNP 10_1101-2020_10_26_351783 256 1 ) ) -RRB- 10_1101-2020_10_26_351783 256 2 ) ) -RRB- 10_1101-2020_10_26_351783 256 3 , , , 10_1101-2020_10_26_351783 256 4 the the DT 10_1101-2020_10_26_351783 256 5 Center Center NNP 10_1101-2020_10_26_351783 256 6 for for IN 10_1101-2020_10_26_351783 256 7 Industrial Industrial NNP 10_1101-2020_10_26_351783 256 8 IT IT NNP 10_1101-2020_10_26_351783 256 9 ( ( -LRB- 10_1101-2020_10_26_351783 256 10 CENIIT)(M.G. CENIIT)(M.G. . 10_1101-2020_10_26_351783 257 1 ) ) -RRB- 10_1101-2020_10_26_351783 257 2 , , , 10_1101-2020_10_26_351783 257 3 European European NNP 10_1101-2020_10_26_351783 257 4 Union Union NNP 10_1101-2020_10_26_351783 257 5 Horizon Horizon NNP 10_1101-2020_10_26_351783 257 6 2020 2020 CD 10_1101-2020_10_26_351783 257 7 / / SYM 10_1101-2020_10_26_351783 257 8 European European NNP 10_1101-2020_10_26_351783 257 9 Research Research NNP 10_1101-2020_10_26_351783 257 10 Council Council NNP 10_1101-2020_10_26_351783 257 11 Consolidator Consolidator NNP 10_1101-2020_10_26_351783 257 12 grant grant NN 10_1101-2020_10_26_351783 257 13 ( ( -LRB- 10_1101-2020_10_26_351783 257 14 Epi4MS epi4ms NN 10_1101-2020_10_26_351783 257 15 , , , 10_1101-2020_10_26_351783 257 16 grant grant VB 10_1101-2020_10_26_351783 257 17 818170(M.J. 818170(m.j. CD 10_1101-2020_10_26_351783 257 18 ) ) -RRB- 10_1101-2020_10_26_351783 257 19 ) ) -RRB- 10_1101-2020_10_26_351783 257 20 , , , 10_1101-2020_10_26_351783 257 21 Knut Knut NNP 10_1101-2020_10_26_351783 257 22 and and CC 10_1101-2020_10_26_351783 257 23 Alice Alice NNP 10_1101-2020_10_26_351783 257 24 Wallenberg Wallenberg NNP 10_1101-2020_10_26_351783 257 25 Foundation Foundation NNP 10_1101-2020_10_26_351783 257 26 ( ( -LRB- 10_1101-2020_10_26_351783 257 27 grant grant NNP 10_1101-2020_10_26_351783 257 28 2019.0089(M.J. 2019.0089(m.j. CD 10_1101-2020_10_26_351783 257 29 ) ) -RRB- 10_1101-2020_10_26_351783 257 30 ) ) -RRB- 10_1101-2020_10_26_351783 257 31 and and CC 10_1101-2020_10_26_351783 257 32 the the DT 10_1101-2020_10_26_351783 257 33 Knowledge Knowledge NNP 10_1101-2020_10_26_351783 257 34 Foundation Foundation NNP 10_1101-2020_10_26_351783 257 35 ( ( -LRB- 10_1101-2020_10_26_351783 257 36 grant grant NNP 10_1101-2020_10_26_351783 257 37 20170298 20170298 CD 10_1101-2020_10_26_351783 257 38 ( ( -LRB- 10_1101-2020_10_26_351783 257 39 Z.L. Z.L. NNP 10_1101-2020_10_26_351783 257 40 ) ) -RRB- 10_1101-2020_10_26_351783 257 41 ) ) -RRB- 10_1101-2020_10_26_351783 257 42 . . . 10_1101-2020_10_26_351783 258 1 Computational computational JJ 10_1101-2020_10_26_351783 258 2 resources resource NNS 10_1101-2020_10_26_351783 258 3 were be VBD 10_1101-2020_10_26_351783 258 4 granted grant VBN 10_1101-2020_10_26_351783 258 5 by by IN 10_1101-2020_10_26_351783 258 6 Swedish swedish JJ 10_1101-2020_10_26_351783 258 7 National National NNP 10_1101-2020_10_26_351783 258 8 Infrastructure Infrastructure NNP 10_1101-2020_10_26_351783 258 9 for for IN 10_1101-2020_10_26_351783 258 10 Computing Computing NNP 10_1101-2020_10_26_351783 258 11 ( ( -LRB- 10_1101-2020_10_26_351783 258 12 SNIC SNIC NNP 10_1101-2020_10_26_351783 258 13 ; ; : 10_1101-2020_10_26_351783 258 14 SNIC SNIC NNP 10_1101-2020_10_26_351783 258 15 2020/5 2020/5 CD 10_1101-2020_10_26_351783 258 16 - - SYM 10_1101-2020_10_26_351783 258 17 177 177 CD 10_1101-2020_10_26_351783 258 18 , , , 10_1101-2020_10_26_351783 258 19 LiU-2018 LiU-2018 NNP 10_1101-2020_10_26_351783 258 20 - - HYPH 10_1101-2020_10_26_351783 258 21 12 12 NNP 10_1101-2020_10_26_351783 258 22 and and CC 10_1101-2020_10_26_351783 258 23 LiU-2019- LiU-2019- NNP 10_1101-2020_10_26_351783 258 24 25 25 CD 10_1101-2020_10_26_351783 258 25 ) ) -RRB- 10_1101-2020_10_26_351783 258 26 . . . 10_1101-2020_10_26_351783 259 1 AUTHOR AUTHOR NNP 10_1101-2020_10_26_351783 259 2 CONTRIBUTIONS contributions NN 10_1101-2020_10_26_351783 259 3 T.V.S.B. t.v.s.b. NN 10_1101-2020_10_26_351783 260 1 compiled compile VBD 10_1101-2020_10_26_351783 260 2 the the DT 10_1101-2020_10_26_351783 260 3 necessary necessary JJ 10_1101-2020_10_26_351783 260 4 data datum NNS 10_1101-2020_10_26_351783 260 5 for for IN 10_1101-2020_10_26_351783 260 6 the the DT 10_1101-2020_10_26_351783 260 7 benchmark benchmark JJ 10_1101-2020_10_26_351783 260 8 analysis analysis NN 10_1101-2020_10_26_351783 260 9 . . . 10_1101-2020_10_26_351783 261 1 H.A.W. H.A.W. NNP 10_1101-2020_10_26_351783 262 1 performed perform VBD 10_1101-2020_10_26_351783 262 2 the the DT 10_1101-2020_10_26_351783 262 3 transcriptomic transcriptomic NNP 10_1101-2020_10_26_351783 262 4 benchmark benchmark NN 10_1101-2020_10_26_351783 262 5 analysis analysis NN 10_1101-2020_10_26_351783 262 6 . . . 10_1101-2020_10_26_351783 263 1 T.V.S.B. t.v.s.b. XX 10_1101-2020_10_26_351783 264 1 performed perform VBD 10_1101-2020_10_26_351783 264 2 the the DT 10_1101-2020_10_26_351783 264 3 methylation methylation NN 10_1101-2020_10_26_351783 264 4 benchmark benchmark NN 10_1101-2020_10_26_351783 264 5 analysis analysis NN 10_1101-2020_10_26_351783 264 6 . . . 10_1101-2020_10_26_351783 265 1 D.M.E. D.M.E. NNP 10_1101-2020_10_26_351783 266 1 and and CC 10_1101-2020_10_26_351783 266 2 H.A.W. H.A.W. NNP 10_1101-2020_10_26_351783 267 1 performed perform VBD 10_1101-2020_10_26_351783 267 2 the the DT 10_1101-2020_10_26_351783 267 3 MS MS NNP 10_1101-2020_10_26_351783 267 4 use use VB 10_1101-2020_10_26_351783 267 5 case case NN 10_1101-2020_10_26_351783 267 6 analysis analysis NN 10_1101-2020_10_26_351783 267 7 . . . 10_1101-2020_10_26_351783 268 1 D.M.E D.M.E NNP 10_1101-2020_10_26_351783 268 2 performed perform VBD 10_1101-2020_10_26_351783 268 3 the the DT 10_1101-2020_10_26_351783 268 4 risk risk NN 10_1101-2020_10_26_351783 268 5 factor factor NN 10_1101-2020_10_26_351783 268 6 analysis analysis NN 10_1101-2020_10_26_351783 268 7 . . . 10_1101-2020_10_26_351783 269 1 ( ( -LRB- 10_1101-2020_10_26_351783 269 2 which which WDT 10_1101-2020_10_26_351783 269 3 was be VBD 10_1101-2020_10_26_351783 269 4 not not RB 10_1101-2020_10_26_351783 269 5 certified certify VBN 10_1101-2020_10_26_351783 269 6 by by IN 10_1101-2020_10_26_351783 269 7 peer peer NN 10_1101-2020_10_26_351783 269 8 review review NN 10_1101-2020_10_26_351783 269 9 ) ) -RRB- 10_1101-2020_10_26_351783 269 10 is be VBZ 10_1101-2020_10_26_351783 269 11 the the DT 10_1101-2020_10_26_351783 269 12 author author NN 10_1101-2020_10_26_351783 269 13 / / SYM 10_1101-2020_10_26_351783 269 14 funder funder NN 10_1101-2020_10_26_351783 269 15 . . . 10_1101-2020_10_26_351783 270 1 All all DT 10_1101-2020_10_26_351783 270 2 rights right NNS 10_1101-2020_10_26_351783 270 3 reserved reserve VBD 10_1101-2020_10_26_351783 270 4 . . . 10_1101-2020_10_26_351783 271 1 No no DT 10_1101-2020_10_26_351783 271 2 reuse reuse NN 10_1101-2020_10_26_351783 271 3 allowed allow VBN 10_1101-2020_10_26_351783 271 4 without without IN 10_1101-2020_10_26_351783 271 5 permission permission NN 10_1101-2020_10_26_351783 271 6 . . . 10_1101-2020_10_26_351783 272 1 The the DT 10_1101-2020_10_26_351783 272 2 copyright copyright NN 10_1101-2020_10_26_351783 272 3 holder holder NN 10_1101-2020_10_26_351783 272 4 for for IN 10_1101-2020_10_26_351783 272 5 this this DT 10_1101-2020_10_26_351783 272 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 272 7 version version NN 10_1101-2020_10_26_351783 272 8 posted post VBD 10_1101-2020_10_26_351783 272 9 January January NNP 10_1101-2020_10_26_351783 272 10 6 6 CD 10_1101-2020_10_26_351783 272 11 , , , 10_1101-2020_10_26_351783 272 12 2021 2021 CD 10_1101-2020_10_26_351783 272 13 . . . 10_1101-2020_10_26_351783 272 14 ; ; : 10_1101-2020_10_26_351783 272 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 272 16 : : : 10_1101-2020_10_26_351783 272 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 272 18 preprint preprint NN 10_1101-2020_10_26_351783 272 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 272 20 19 19 CD 10_1101-2020_10_26_351783 272 21 M.J.,I.K.,T.O. m.j.,i.k.,t.o. CD 10_1101-2020_10_26_351783 272 22 , , , 10_1101-2020_10_26_351783 272 23 and and CC 10_1101-2020_10_26_351783 272 24 L.A. L.A. NNP 10_1101-2020_10_26_351783 272 25 , , , 10_1101-2020_10_26_351783 272 26 provided provide VBD 10_1101-2020_10_26_351783 272 27 the the DT 10_1101-2020_10_26_351783 272 28 raw raw JJ 10_1101-2020_10_26_351783 272 29 data datum NNS 10_1101-2020_10_26_351783 272 30 and and CC 10_1101-2020_10_26_351783 272 31 collected collect VBD 10_1101-2020_10_26_351783 272 32 the the DT 10_1101-2020_10_26_351783 272 33 associated associate VBN 10_1101-2020_10_26_351783 272 34 risk risk NN 10_1101-2020_10_26_351783 272 35 factor factor NN 10_1101-2020_10_26_351783 272 36 data datum NNS 10_1101-2020_10_26_351783 272 37 for for IN 10_1101-2020_10_26_351783 272 38 the the DT 10_1101-2020_10_26_351783 272 39 independent independent JJ 10_1101-2020_10_26_351783 272 40 methylation methylation NN 10_1101-2020_10_26_351783 272 41 dataset dataset NN 10_1101-2020_10_26_351783 272 42 . . . 10_1101-2020_10_26_351783 273 1 T.V.S.B T.V.S.B NNP 10_1101-2020_10_26_351783 273 2 performed perform VBD 10_1101-2020_10_26_351783 273 3 the the DT 10_1101-2020_10_26_351783 273 4 independent independent JJ 10_1101-2020_10_26_351783 273 5 validation validation NN 10_1101-2020_10_26_351783 273 6 dataset dataset NN 10_1101-2020_10_26_351783 273 7 analysis analysis NN 10_1101-2020_10_26_351783 273 8 . . . 10_1101-2020_10_26_351783 274 1 T.V.S.B. t.v.s.b. XX 10_1101-2020_10_26_351783 275 1 and and CC 10_1101-2020_10_26_351783 275 2 D.M.E. D.M.E. NNP 10_1101-2020_10_26_351783 276 1 collectively collectively RB 10_1101-2020_10_26_351783 276 2 made make VBD 10_1101-2020_10_26_351783 276 3 the the DT 10_1101-2020_10_26_351783 276 4 plots plot NNS 10_1101-2020_10_26_351783 276 5 and and CC 10_1101-2020_10_26_351783 276 6 figures figure NNS 10_1101-2020_10_26_351783 276 7 for for IN 10_1101-2020_10_26_351783 276 8 the the DT 10_1101-2020_10_26_351783 276 9 manuscript manuscript NN 10_1101-2020_10_26_351783 276 10 . . . 10_1101-2020_10_26_351783 277 1 M.G. M.G. NNP 10_1101-2020_10_26_351783 278 1 and and CC 10_1101-2020_10_26_351783 278 2 Z.L. Z.L. NNP 10_1101-2020_10_26_351783 279 1 designed design VBN 10_1101-2020_10_26_351783 279 2 the the DT 10_1101-2020_10_26_351783 279 3 study study NN 10_1101-2020_10_26_351783 279 4 . . . 10_1101-2020_10_26_351783 280 1 T.V.S.B. t.v.s.b. XX 10_1101-2020_10_26_351783 281 1 and and CC 10_1101-2020_10_26_351783 281 2 D.M.E. D.M.E. NNP 10_1101-2020_10_26_351783 282 1 prepared prepare VBD 10_1101-2020_10_26_351783 282 2 the the DT 10_1101-2020_10_26_351783 282 3 manuscript manuscript NN 10_1101-2020_10_26_351783 282 4 . . . 10_1101-2020_10_26_351783 283 1 All all DT 10_1101-2020_10_26_351783 283 2 authors author NNS 10_1101-2020_10_26_351783 283 3 discussed discuss VBD 10_1101-2020_10_26_351783 283 4 the the DT 10_1101-2020_10_26_351783 283 5 results result NNS 10_1101-2020_10_26_351783 283 6 and and CC 10_1101-2020_10_26_351783 283 7 commented comment VBN 10_1101-2020_10_26_351783 283 8 on on IN 10_1101-2020_10_26_351783 283 9 the the DT 10_1101-2020_10_26_351783 283 10 manuscript manuscript NN 10_1101-2020_10_26_351783 283 11 at at IN 10_1101-2020_10_26_351783 283 12 all all DT 10_1101-2020_10_26_351783 283 13 stages stage NNS 10_1101-2020_10_26_351783 283 14 . . . 10_1101-2020_10_26_351783 284 1 ( ( -LRB- 10_1101-2020_10_26_351783 284 2 which which WDT 10_1101-2020_10_26_351783 284 3 was be VBD 10_1101-2020_10_26_351783 284 4 not not RB 10_1101-2020_10_26_351783 284 5 certified certify VBN 10_1101-2020_10_26_351783 284 6 by by IN 10_1101-2020_10_26_351783 284 7 peer peer NN 10_1101-2020_10_26_351783 284 8 review review NN 10_1101-2020_10_26_351783 284 9 ) ) -RRB- 10_1101-2020_10_26_351783 284 10 is be VBZ 10_1101-2020_10_26_351783 284 11 the the DT 10_1101-2020_10_26_351783 284 12 author author NN 10_1101-2020_10_26_351783 284 13 / / SYM 10_1101-2020_10_26_351783 284 14 funder funder NN 10_1101-2020_10_26_351783 284 15 . . . 10_1101-2020_10_26_351783 285 1 All all DT 10_1101-2020_10_26_351783 285 2 rights right NNS 10_1101-2020_10_26_351783 285 3 reserved reserve VBD 10_1101-2020_10_26_351783 285 4 . . . 10_1101-2020_10_26_351783 286 1 No no DT 10_1101-2020_10_26_351783 286 2 reuse reuse NN 10_1101-2020_10_26_351783 286 3 allowed allow VBN 10_1101-2020_10_26_351783 286 4 without without IN 10_1101-2020_10_26_351783 286 5 permission permission NN 10_1101-2020_10_26_351783 286 6 . . . 10_1101-2020_10_26_351783 287 1 The the DT 10_1101-2020_10_26_351783 287 2 copyright copyright NN 10_1101-2020_10_26_351783 287 3 holder holder NN 10_1101-2020_10_26_351783 287 4 for for IN 10_1101-2020_10_26_351783 287 5 this this DT 10_1101-2020_10_26_351783 287 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 287 7 version version NN 10_1101-2020_10_26_351783 287 8 posted post VBD 10_1101-2020_10_26_351783 287 9 January January NNP 10_1101-2020_10_26_351783 287 10 6 6 CD 10_1101-2020_10_26_351783 287 11 , , , 10_1101-2020_10_26_351783 287 12 2021 2021 CD 10_1101-2020_10_26_351783 287 13 . . . 10_1101-2020_10_26_351783 287 14 ; ; : 10_1101-2020_10_26_351783 287 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 287 16 : : : 10_1101-2020_10_26_351783 287 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 287 18 preprint preprint NN 10_1101-2020_10_26_351783 287 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 287 20 20 20 CD 10_1101-2020_10_26_351783 287 21 REFERENCES reference NNS 10_1101-2020_10_26_351783 287 22 1 1 CD 10_1101-2020_10_26_351783 287 23 . . . 10_1101-2020_10_26_351783 288 1 Naylor Naylor NNP 10_1101-2020_10_26_351783 288 2 S S NNP 10_1101-2020_10_26_351783 288 3 , , , 10_1101-2020_10_26_351783 288 4 Chen Chen NNP 10_1101-2020_10_26_351783 288 5 JY JY NNP 10_1101-2020_10_26_351783 288 6 . . . 10_1101-2020_10_26_351783 289 1 NIH NIH NNP 10_1101-2020_10_26_351783 289 2 Public Public NNP 10_1101-2020_10_26_351783 289 3 Access Access NNP 10_1101-2020_10_26_351783 289 4 . . . 10_1101-2020_10_26_351783 290 1 Natl Natl NNP 10_1101-2020_10_26_351783 290 2 Institutes Institutes NNP 10_1101-2020_10_26_351783 290 3 Heal Heal NNP 10_1101-2020_10_26_351783 290 4 . . . 10_1101-2020_10_26_351783 291 1 2011;7:275–89 2011;7:275–89 LS 10_1101-2020_10_26_351783 291 2 . . . 10_1101-2020_10_26_351783 292 1 2 2 LS 10_1101-2020_10_26_351783 292 2 . . . 10_1101-2020_10_26_351783 293 1 Santiago Santiago NNP 10_1101-2020_10_26_351783 293 2 JA JA NNP 10_1101-2020_10_26_351783 293 3 , , , 10_1101-2020_10_26_351783 293 4 Bottero Bottero NNP 10_1101-2020_10_26_351783 293 5 V V NNP 10_1101-2020_10_26_351783 293 6 , , , 10_1101-2020_10_26_351783 293 7 Potashkin Potashkin NNP 10_1101-2020_10_26_351783 293 8 JA JA NNP 10_1101-2020_10_26_351783 293 9 . . . 10_1101-2020_10_26_351783 294 1 Dissecting dissect VBG 10_1101-2020_10_26_351783 294 2 the the DT 10_1101-2020_10_26_351783 294 3 Molecular Molecular NNP 10_1101-2020_10_26_351783 294 4 Mechanisms Mechanisms NNPS 10_1101-2020_10_26_351783 294 5 of of IN 10_1101-2020_10_26_351783 294 6 Neurodegenerative Neurodegenerative NNP 10_1101-2020_10_26_351783 294 7 Diseases Diseases NNP 10_1101-2020_10_26_351783 294 8 through through IN 10_1101-2020_10_26_351783 294 9 Network Network NNP 10_1101-2020_10_26_351783 294 10 Biology Biology NNP 10_1101-2020_10_26_351783 294 11 . . . 10_1101-2020_10_26_351783 295 1 Front front JJ 10_1101-2020_10_26_351783 295 2 Aging age VBG 10_1101-2020_10_26_351783 295 3 Neurosci Neurosci NNP 10_1101-2020_10_26_351783 295 4 [ [ -LRB- 10_1101-2020_10_26_351783 295 5 Internet internet NN 10_1101-2020_10_26_351783 295 6 ] ] -RRB- 10_1101-2020_10_26_351783 295 7 . . . 10_1101-2020_10_26_351783 296 1 2017;9:1–13 2017;9:1–13 LS 10_1101-2020_10_26_351783 296 2 . . . 10_1101-2020_10_26_351783 297 1 Available available JJ 10_1101-2020_10_26_351783 297 2 from from IN 10_1101-2020_10_26_351783 297 3 : : : 10_1101-2020_10_26_351783 297 4 http://journal.frontiersin.org/article/10.3389/fnagi.2017.00166/full http://journal.frontiersin.org/article/10.3389/fnagi.2017.00166/full ADD 10_1101-2020_10_26_351783 297 5 3 3 CD 10_1101-2020_10_26_351783 297 6 . . . 10_1101-2020_10_26_351783 298 1 Barabási Barabási NNP 10_1101-2020_10_26_351783 298 2 AL AL NNP 10_1101-2020_10_26_351783 298 3 , , , 10_1101-2020_10_26_351783 298 4 Gulbahce Gulbahce NNP 10_1101-2020_10_26_351783 298 5 N N NNP 10_1101-2020_10_26_351783 298 6 , , , 10_1101-2020_10_26_351783 298 7 Loscalzo Loscalzo NNP 10_1101-2020_10_26_351783 298 8 J. J. NNP 10_1101-2020_10_26_351783 299 1 Network network NN 10_1101-2020_10_26_351783 299 2 medicine medicine NN 10_1101-2020_10_26_351783 299 3 : : : 10_1101-2020_10_26_351783 299 4 A a DT 10_1101-2020_10_26_351783 299 5 network network NN 10_1101-2020_10_26_351783 299 6 - - HYPH 10_1101-2020_10_26_351783 299 7 based base VBN 10_1101-2020_10_26_351783 299 8 approach approach NN 10_1101-2020_10_26_351783 299 9 to to IN 10_1101-2020_10_26_351783 299 10 human human JJ 10_1101-2020_10_26_351783 299 11 disease disease NN 10_1101-2020_10_26_351783 299 12 . . . 10_1101-2020_10_26_351783 300 1 Nat Nat NNP 10_1101-2020_10_26_351783 300 2 Rev Rev NNP 10_1101-2020_10_26_351783 300 3 Genet Genet NNP 10_1101-2020_10_26_351783 300 4 [ [ -LRB- 10_1101-2020_10_26_351783 300 5 Internet internet NN 10_1101-2020_10_26_351783 300 6 ] ] -RRB- 10_1101-2020_10_26_351783 300 7 . . . 10_1101-2020_10_26_351783 301 1 Nature Nature NNP 10_1101-2020_10_26_351783 301 2 Publishing Publishing NNP 10_1101-2020_10_26_351783 301 3 Group Group NNP 10_1101-2020_10_26_351783 301 4 ; ; : 10_1101-2020_10_26_351783 301 5 2011;12:56–68 2011;12:56–68 CD 10_1101-2020_10_26_351783 301 6 . . . 10_1101-2020_10_26_351783 302 1 Available available JJ 10_1101-2020_10_26_351783 302 2 from from IN 10_1101-2020_10_26_351783 302 3 : : : 10_1101-2020_10_26_351783 302 4 http://dx.doi.org/10.1038/nrg2918 http://dx.doi.org/10.1038/nrg2918 NNP 10_1101-2020_10_26_351783 302 5 4 4 CD 10_1101-2020_10_26_351783 302 6 . . . 10_1101-2020_10_26_351783 303 1 Gustafsson Gustafsson NNP 10_1101-2020_10_26_351783 303 2 M M NNP 10_1101-2020_10_26_351783 303 3 , , , 10_1101-2020_10_26_351783 303 4 Nestor Nestor NNP 10_1101-2020_10_26_351783 303 5 CE CE NNP 10_1101-2020_10_26_351783 303 6 , , , 10_1101-2020_10_26_351783 303 7 Zhang Zhang NNP 10_1101-2020_10_26_351783 303 8 H H NNP 10_1101-2020_10_26_351783 303 9 , , , 10_1101-2020_10_26_351783 303 10 Barabási Barabási NNP 10_1101-2020_10_26_351783 303 11 A A NNP 10_1101-2020_10_26_351783 303 12 - - HYPH 10_1101-2020_10_26_351783 303 13 L L NNP 10_1101-2020_10_26_351783 303 14 , , , 10_1101-2020_10_26_351783 303 15 Baranzini Baranzini NNP 10_1101-2020_10_26_351783 303 16 S S NNP 10_1101-2020_10_26_351783 303 17 , , , 10_1101-2020_10_26_351783 303 18 Brunak Brunak NNP 10_1101-2020_10_26_351783 303 19 S S NNP 10_1101-2020_10_26_351783 303 20 , , , 10_1101-2020_10_26_351783 303 21 et et NNP 10_1101-2020_10_26_351783 303 22 al al NNP 10_1101-2020_10_26_351783 303 23 . . . 10_1101-2020_10_26_351783 304 1 Modules module NNS 10_1101-2020_10_26_351783 304 2 , , , 10_1101-2020_10_26_351783 304 3 networks network NNS 10_1101-2020_10_26_351783 304 4 and and CC 10_1101-2020_10_26_351783 304 5 systems system NNS 10_1101-2020_10_26_351783 304 6 medicine medicine NN 10_1101-2020_10_26_351783 304 7 for for IN 10_1101-2020_10_26_351783 304 8 understanding understanding NN 10_1101-2020_10_26_351783 304 9 disease disease NN 10_1101-2020_10_26_351783 304 10 and and CC 10_1101-2020_10_26_351783 304 11 aiding aid VBG 10_1101-2020_10_26_351783 304 12 diagnosis diagnosis NN 10_1101-2020_10_26_351783 304 13 . . . 10_1101-2020_10_26_351783 305 1 Genome genome JJ 10_1101-2020_10_26_351783 305 2 Med Med NNP 10_1101-2020_10_26_351783 305 3 [ [ -LRB- 10_1101-2020_10_26_351783 305 4 Internet internet NN 10_1101-2020_10_26_351783 305 5 ] ] -RRB- 10_1101-2020_10_26_351783 305 6 . . . 10_1101-2020_10_26_351783 306 1 2014;6:82 2014;6:82 CD 10_1101-2020_10_26_351783 306 2 . . . 10_1101-2020_10_26_351783 307 1 Available available JJ 10_1101-2020_10_26_351783 307 2 from from IN 10_1101-2020_10_26_351783 307 3 : : : 10_1101-2020_10_26_351783 307 4 http://genomemedicine.biomedcentral.com/articles/10.1186/s13073- http://genomemedicine.biomedcentral.com/articles/10.1186/s13073- NNP 10_1101-2020_10_26_351783 307 5 014 014 CD 10_1101-2020_10_26_351783 307 6 - - HYPH 10_1101-2020_10_26_351783 307 7 0082 0082 CD 10_1101-2020_10_26_351783 307 8 - - HYPH 10_1101-2020_10_26_351783 307 9 6 6 CD 10_1101-2020_10_26_351783 307 10 5 5 CD 10_1101-2020_10_26_351783 307 11 . . . 10_1101-2020_10_26_351783 308 1 Szklarczyk Szklarczyk NNP 10_1101-2020_10_26_351783 308 2 D D NNP 10_1101-2020_10_26_351783 308 3 , , , 10_1101-2020_10_26_351783 308 4 Gable Gable NNP 10_1101-2020_10_26_351783 308 5 AL AL NNP 10_1101-2020_10_26_351783 308 6 , , , 10_1101-2020_10_26_351783 308 7 Lyon Lyon NNP 10_1101-2020_10_26_351783 308 8 D D NNP 10_1101-2020_10_26_351783 308 9 , , , 10_1101-2020_10_26_351783 308 10 Junge Junge NNP 10_1101-2020_10_26_351783 308 11 A A NNP 10_1101-2020_10_26_351783 308 12 , , , 10_1101-2020_10_26_351783 308 13 Wyder Wyder NNP 10_1101-2020_10_26_351783 308 14 S S NNP 10_1101-2020_10_26_351783 308 15 , , , 10_1101-2020_10_26_351783 308 16 Huerta Huerta NNP 10_1101-2020_10_26_351783 308 17 - - HYPH 10_1101-2020_10_26_351783 308 18 cepas cepas NNP 10_1101-2020_10_26_351783 308 19 J J NNP 10_1101-2020_10_26_351783 308 20 , , , 10_1101-2020_10_26_351783 308 21 et et NNP 10_1101-2020_10_26_351783 308 22 al al NNP 10_1101-2020_10_26_351783 308 23 . . . 10_1101-2020_10_26_351783 309 1 STRING string NN 10_1101-2020_10_26_351783 309 2 v11 v11 NN 10_1101-2020_10_26_351783 309 3 [ [ -LRB- 10_1101-2020_10_26_351783 309 4 : : : 10_1101-2020_10_26_351783 309 5 protein protein NN 10_1101-2020_10_26_351783 309 6 – – : 10_1101-2020_10_26_351783 309 7 protein protein NNP 10_1101-2020_10_26_351783 309 8 association association NNP 10_1101-2020_10_26_351783 309 9 networks network NNS 10_1101-2020_10_26_351783 309 10 with with IN 10_1101-2020_10_26_351783 309 11 increased increase VBN 10_1101-2020_10_26_351783 309 12 coverage coverage NN 10_1101-2020_10_26_351783 309 13 , , , 10_1101-2020_10_26_351783 309 14 supporting support VBG 10_1101-2020_10_26_351783 309 15 functional functional JJ 10_1101-2020_10_26_351783 309 16 discovery discovery NN 10_1101-2020_10_26_351783 309 17 in in IN 10_1101-2020_10_26_351783 309 18 genome- genome- NN 10_1101-2020_10_26_351783 309 19 wide wide JJ 10_1101-2020_10_26_351783 309 20 experimental experimental JJ 10_1101-2020_10_26_351783 309 21 datasets dataset NNS 10_1101-2020_10_26_351783 309 22 . . . 10_1101-2020_10_26_351783 310 1 Oxford Oxford NNP 10_1101-2020_10_26_351783 310 2 University University NNP 10_1101-2020_10_26_351783 310 3 Press Press NNP 10_1101-2020_10_26_351783 310 4 ; ; : 10_1101-2020_10_26_351783 310 5 2019;47:607–13 2019;47:607–13 NNP 10_1101-2020_10_26_351783 310 6 . . . 10_1101-2020_10_26_351783 311 1 6 6 CD 10_1101-2020_10_26_351783 311 2 . . . 10_1101-2020_10_26_351783 312 1 Lamparter lamparter NN 10_1101-2020_10_26_351783 312 2 D D NNP 10_1101-2020_10_26_351783 312 3 , , , 10_1101-2020_10_26_351783 312 4 Lin Lin NNP 10_1101-2020_10_26_351783 312 5 J J NNP 10_1101-2020_10_26_351783 312 6 , , , 10_1101-2020_10_26_351783 312 7 Kutalik Kutalik NNP 10_1101-2020_10_26_351783 312 8 Z Z NNP 10_1101-2020_10_26_351783 312 9 , , , 10_1101-2020_10_26_351783 312 10 Choobdar Choobdar NNP 10_1101-2020_10_26_351783 312 11 S S NNP 10_1101-2020_10_26_351783 312 12 , , , 10_1101-2020_10_26_351783 312 13 Hescott Hescott NNP 10_1101-2020_10_26_351783 312 14 B B NNP 10_1101-2020_10_26_351783 312 15 , , , 10_1101-2020_10_26_351783 312 16 Tomasoni Tomasoni NNP 10_1101-2020_10_26_351783 312 17 M M NNP 10_1101-2020_10_26_351783 312 18 , , , 10_1101-2020_10_26_351783 312 19 et et NNP 10_1101-2020_10_26_351783 312 20 al al NNP 10_1101-2020_10_26_351783 312 21 . . . 10_1101-2020_10_26_351783 313 1 Open Open NNP 10_1101-2020_10_26_351783 313 2 Community Community NNP 10_1101-2020_10_26_351783 313 3 Challenge Challenge NNP 10_1101-2020_10_26_351783 313 4 Reveals reveal VBZ 10_1101-2020_10_26_351783 313 5 Molecular Molecular NNP 10_1101-2020_10_26_351783 313 6 Network Network NNP 10_1101-2020_10_26_351783 313 7 Modules Modules NNP 10_1101-2020_10_26_351783 313 8 with with IN 10_1101-2020_10_26_351783 313 9 Key Key NNP 10_1101-2020_10_26_351783 313 10 Roles Roles NNPS 10_1101-2020_10_26_351783 313 11 in in IN 10_1101-2020_10_26_351783 313 12 Diseases Diseases NNP 10_1101-2020_10_26_351783 313 13 . . . 10_1101-2020_10_26_351783 314 1 SSRN SSRN NNP 10_1101-2020_10_26_351783 314 2 Electron Electron NNP 10_1101-2020_10_26_351783 314 3 J. J. NNP 10_1101-2020_10_26_351783 315 1 2018;1 2018;1 LS 10_1101-2020_10_26_351783 315 2 – – : 10_1101-2020_10_26_351783 315 3 63 63 CD 10_1101-2020_10_26_351783 315 4 . . . 10_1101-2020_10_26_351783 316 1 7 7 LS 10_1101-2020_10_26_351783 316 2 . . . 10_1101-2020_10_26_351783 317 1 Schadt Schadt NNP 10_1101-2020_10_26_351783 317 2 EE EE NNP 10_1101-2020_10_26_351783 317 3 . . . 10_1101-2020_10_26_351783 318 1 Molecular molecular JJ 10_1101-2020_10_26_351783 318 2 networks network NNS 10_1101-2020_10_26_351783 318 3 as as IN 10_1101-2020_10_26_351783 318 4 sensors sensor NNS 10_1101-2020_10_26_351783 318 5 and and CC 10_1101-2020_10_26_351783 318 6 drivers driver NNS 10_1101-2020_10_26_351783 318 7 of of IN 10_1101-2020_10_26_351783 318 8 common common JJ 10_1101-2020_10_26_351783 318 9 human human JJ 10_1101-2020_10_26_351783 318 10 diseases disease NNS 10_1101-2020_10_26_351783 318 11 . . . 10_1101-2020_10_26_351783 319 1 Nature nature NN 10_1101-2020_10_26_351783 319 2 [ [ -LRB- 10_1101-2020_10_26_351783 319 3 Internet internet NN 10_1101-2020_10_26_351783 319 4 ] ] -RRB- 10_1101-2020_10_26_351783 319 5 . . . 10_1101-2020_10_26_351783 320 1 2009;461:218–23 2009;461:218–23 CD 10_1101-2020_10_26_351783 320 2 . . . 10_1101-2020_10_26_351783 321 1 Available available JJ 10_1101-2020_10_26_351783 321 2 from from IN 10_1101-2020_10_26_351783 321 3 : : : 10_1101-2020_10_26_351783 321 4 http://www.nature.com/doifinder/10.1038/nature08454 http://www.nature.com/doifinder/10.1038/nature08454 NNP 10_1101-2020_10_26_351783 321 5 8 8 CD 10_1101-2020_10_26_351783 321 6 . . . 10_1101-2020_10_26_351783 322 1 Ghiassian ghiassian JJ 10_1101-2020_10_26_351783 322 2 SD SD NNP 10_1101-2020_10_26_351783 322 3 , , , 10_1101-2020_10_26_351783 322 4 Menche Menche NNP 10_1101-2020_10_26_351783 322 5 J J NNP 10_1101-2020_10_26_351783 322 6 , , , 10_1101-2020_10_26_351783 322 7 Barabási Barabási NNP 10_1101-2020_10_26_351783 322 8 AL AL NNP 10_1101-2020_10_26_351783 322 9 . . . 10_1101-2020_10_26_351783 323 1 A a DT 10_1101-2020_10_26_351783 323 2 DIseAse disease NN 10_1101-2020_10_26_351783 323 3 MOdule MOdule NNP 10_1101-2020_10_26_351783 323 4 Detection detection NN 10_1101-2020_10_26_351783 323 5 ( ( -LRB- 10_1101-2020_10_26_351783 323 6 DIAMOnD diamond NN 10_1101-2020_10_26_351783 323 7 ) ) -RRB- 10_1101-2020_10_26_351783 323 8 Algorithm Algorithm NNP 10_1101-2020_10_26_351783 323 9 Derived derive VBN 10_1101-2020_10_26_351783 323 10 from from IN 10_1101-2020_10_26_351783 323 11 a a DT 10_1101-2020_10_26_351783 323 12 Systematic Systematic NNP 10_1101-2020_10_26_351783 323 13 Analysis Analysis NNP 10_1101-2020_10_26_351783 323 14 of of IN 10_1101-2020_10_26_351783 323 15 Connectivity Connectivity NNP 10_1101-2020_10_26_351783 323 16 Patterns Patterns NNPS 10_1101-2020_10_26_351783 323 17 of of IN 10_1101-2020_10_26_351783 323 18 Disease Disease NNP 10_1101-2020_10_26_351783 323 19 Proteins Proteins NNPS 10_1101-2020_10_26_351783 323 20 in in IN 10_1101-2020_10_26_351783 323 21 the the DT 10_1101-2020_10_26_351783 323 22 Human Human NNP 10_1101-2020_10_26_351783 323 23 Interactome Interactome NNP 10_1101-2020_10_26_351783 323 24 . . . 10_1101-2020_10_26_351783 324 1 Rzhetsky Rzhetsky NNP 10_1101-2020_10_26_351783 324 2 A A NNP 10_1101-2020_10_26_351783 324 3 , , , 10_1101-2020_10_26_351783 324 4 editor editor NN 10_1101-2020_10_26_351783 324 5 . . . 10_1101-2020_10_26_351783 325 1 PLoS PLoS : 10_1101-2020_10_26_351783 325 2 Comput comput NN 10_1101-2020_10_26_351783 325 3 Biol Biol NNP 10_1101-2020_10_26_351783 325 4 [ [ -LRB- 10_1101-2020_10_26_351783 325 5 Internet internet NN 10_1101-2020_10_26_351783 325 6 ] ] -RRB- 10_1101-2020_10_26_351783 325 7 . . . 10_1101-2020_10_26_351783 326 1 2015;11 2015;11 CD 10_1101-2020_10_26_351783 326 2 : : : 10_1101-2020_10_26_351783 326 3 e1004120 e1004120 NNP 10_1101-2020_10_26_351783 326 4 . . . 10_1101-2020_10_26_351783 327 1 Available available JJ 10_1101-2020_10_26_351783 327 2 from from IN 10_1101-2020_10_26_351783 327 3 : : : 10_1101-2020_10_26_351783 327 4 ( ( -LRB- 10_1101-2020_10_26_351783 327 5 which which WDT 10_1101-2020_10_26_351783 327 6 was be VBD 10_1101-2020_10_26_351783 327 7 not not RB 10_1101-2020_10_26_351783 327 8 certified certify VBN 10_1101-2020_10_26_351783 327 9 by by IN 10_1101-2020_10_26_351783 327 10 peer peer NN 10_1101-2020_10_26_351783 327 11 review review NN 10_1101-2020_10_26_351783 327 12 ) ) -RRB- 10_1101-2020_10_26_351783 327 13 is be VBZ 10_1101-2020_10_26_351783 327 14 the the DT 10_1101-2020_10_26_351783 327 15 author author NN 10_1101-2020_10_26_351783 327 16 / / SYM 10_1101-2020_10_26_351783 327 17 funder funder NN 10_1101-2020_10_26_351783 327 18 . . . 10_1101-2020_10_26_351783 328 1 All all DT 10_1101-2020_10_26_351783 328 2 rights right NNS 10_1101-2020_10_26_351783 328 3 reserved reserve VBD 10_1101-2020_10_26_351783 328 4 . . . 10_1101-2020_10_26_351783 329 1 No no DT 10_1101-2020_10_26_351783 329 2 reuse reuse NN 10_1101-2020_10_26_351783 329 3 allowed allow VBN 10_1101-2020_10_26_351783 329 4 without without IN 10_1101-2020_10_26_351783 329 5 permission permission NN 10_1101-2020_10_26_351783 329 6 . . . 10_1101-2020_10_26_351783 330 1 The the DT 10_1101-2020_10_26_351783 330 2 copyright copyright NN 10_1101-2020_10_26_351783 330 3 holder holder NN 10_1101-2020_10_26_351783 330 4 for for IN 10_1101-2020_10_26_351783 330 5 this this DT 10_1101-2020_10_26_351783 330 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 330 7 version version NN 10_1101-2020_10_26_351783 330 8 posted post VBD 10_1101-2020_10_26_351783 330 9 January January NNP 10_1101-2020_10_26_351783 330 10 6 6 CD 10_1101-2020_10_26_351783 330 11 , , , 10_1101-2020_10_26_351783 330 12 2021 2021 CD 10_1101-2020_10_26_351783 330 13 . . . 10_1101-2020_10_26_351783 330 14 ; ; : 10_1101-2020_10_26_351783 330 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 330 16 : : : 10_1101-2020_10_26_351783 330 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 330 18 preprint preprint NN 10_1101-2020_10_26_351783 330 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 330 20 21 21 CD 10_1101-2020_10_26_351783 330 21 https://dx.plos.org/10.1371/journal.pcbi.1004120 https://dx.plos.org/10.1371/journal.pcbi.1004120 CD 10_1101-2020_10_26_351783 330 22 9 9 CD 10_1101-2020_10_26_351783 330 23 . . . 10_1101-2020_10_26_351783 331 1 Hellberg Hellberg NNP 10_1101-2020_10_26_351783 331 2 S S NNP 10_1101-2020_10_26_351783 331 3 , , , 10_1101-2020_10_26_351783 331 4 Eklund Eklund NNP 10_1101-2020_10_26_351783 331 5 D D NNP 10_1101-2020_10_26_351783 331 6 , , , 10_1101-2020_10_26_351783 331 7 Gawel Gawel NNP 10_1101-2020_10_26_351783 331 8 DR DR NNP 10_1101-2020_10_26_351783 331 9 , , , 10_1101-2020_10_26_351783 331 10 Köpsén Köpsén NNP 10_1101-2020_10_26_351783 331 11 M M NNP 10_1101-2020_10_26_351783 331 12 , , , 10_1101-2020_10_26_351783 331 13 Zhang Zhang NNP 10_1101-2020_10_26_351783 331 14 H H NNP 10_1101-2020_10_26_351783 331 15 , , , 10_1101-2020_10_26_351783 331 16 Nestor Nestor NNP 10_1101-2020_10_26_351783 331 17 CE CE NNP 10_1101-2020_10_26_351783 331 18 , , , 10_1101-2020_10_26_351783 331 19 et et NNP 10_1101-2020_10_26_351783 331 20 al al NNP 10_1101-2020_10_26_351783 331 21 . . . 10_1101-2020_10_26_351783 332 1 Dynamic Dynamic NNP 10_1101-2020_10_26_351783 332 2 Response Response NNP 10_1101-2020_10_26_351783 332 3 Genes Genes NNPS 10_1101-2020_10_26_351783 332 4 in in IN 10_1101-2020_10_26_351783 332 5 CD4 CD4 NNP 10_1101-2020_10_26_351783 332 6 + + SYM 10_1101-2020_10_26_351783 332 7 T t NN 10_1101-2020_10_26_351783 332 8 Cells cell NNS 10_1101-2020_10_26_351783 332 9 Reveal reveal VBP 10_1101-2020_10_26_351783 332 10 a a DT 10_1101-2020_10_26_351783 332 11 Network Network NNP 10_1101-2020_10_26_351783 332 12 of of IN 10_1101-2020_10_26_351783 332 13 Interactive Interactive NNP 10_1101-2020_10_26_351783 332 14 Proteins Proteins NNPS 10_1101-2020_10_26_351783 332 15 that that IN 10_1101-2020_10_26_351783 332 16 Classifies Classifies NNPS 10_1101-2020_10_26_351783 332 17 Disease Disease NNP 10_1101-2020_10_26_351783 332 18 Activity Activity NNP 10_1101-2020_10_26_351783 332 19 in in IN 10_1101-2020_10_26_351783 332 20 Multiple Multiple NNP 10_1101-2020_10_26_351783 332 21 Sclerosis Sclerosis NNP 10_1101-2020_10_26_351783 332 22 . . . 10_1101-2020_10_26_351783 333 1 Cell Cell NNP 10_1101-2020_10_26_351783 333 2 Rep. Rep. NNP 10_1101-2020_10_26_351783 333 3 2016;16:2928–39 2016;16:2928–39 CD 10_1101-2020_10_26_351783 333 4 . . . 10_1101-2020_10_26_351783 334 1 10 10 CD 10_1101-2020_10_26_351783 334 2 . . . 10_1101-2020_10_26_351783 335 1 Wang Wang NNP 10_1101-2020_10_26_351783 335 2 H H NNP 10_1101-2020_10_26_351783 335 3 , , , 10_1101-2020_10_26_351783 335 4 Rogers Rogers NNP 10_1101-2020_10_26_351783 335 5 G G NNP 10_1101-2020_10_26_351783 335 6 , , , 10_1101-2020_10_26_351783 335 7 Benson Benson NNP 10_1101-2020_10_26_351783 335 8 M M NNP 10_1101-2020_10_26_351783 335 9 , , , 10_1101-2020_10_26_351783 335 10 Jarvelin Jarvelin NNP 10_1101-2020_10_26_351783 335 11 M M NNP 10_1101-2020_10_26_351783 335 12 - - HYPH 10_1101-2020_10_26_351783 335 13 R R NNP 10_1101-2020_10_26_351783 335 14 , , , 10_1101-2020_10_26_351783 335 15 Chavali Chavali NNP 10_1101-2020_10_26_351783 335 16 S S NNP 10_1101-2020_10_26_351783 335 17 , , , 10_1101-2020_10_26_351783 335 18 Ramasamy Ramasamy NNP 10_1101-2020_10_26_351783 335 19 A A NNP 10_1101-2020_10_26_351783 335 20 , , , 10_1101-2020_10_26_351783 335 21 et et NNP 10_1101-2020_10_26_351783 335 22 al al NNP 10_1101-2020_10_26_351783 335 23 . . . 10_1101-2020_10_26_351783 336 1 Highly highly RB 10_1101-2020_10_26_351783 336 2 interconnected interconnect VBN 10_1101-2020_10_26_351783 336 3 genes gene NNS 10_1101-2020_10_26_351783 336 4 in in IN 10_1101-2020_10_26_351783 336 5 disease disease NN 10_1101-2020_10_26_351783 336 6 - - HYPH 10_1101-2020_10_26_351783 336 7 specific specific JJ 10_1101-2020_10_26_351783 336 8 networks network NNS 10_1101-2020_10_26_351783 336 9 are be VBP 10_1101-2020_10_26_351783 336 10 enriched enrich VBN 10_1101-2020_10_26_351783 336 11 for for IN 10_1101-2020_10_26_351783 336 12 disease disease NN 10_1101-2020_10_26_351783 336 13 - - HYPH 10_1101-2020_10_26_351783 336 14 associated associate VBN 10_1101-2020_10_26_351783 336 15 polymorphisms polymorphism NNS 10_1101-2020_10_26_351783 336 16 . . . 10_1101-2020_10_26_351783 337 1 Genome Genome NNP 10_1101-2020_10_26_351783 337 2 Biol Biol NNP 10_1101-2020_10_26_351783 337 3 . . . 10_1101-2020_10_26_351783 338 1 2012;13 2012;13 CD 10_1101-2020_10_26_351783 338 2 : : : 10_1101-2020_10_26_351783 338 3 R46 R46 NNP 10_1101-2020_10_26_351783 338 4 . . . 10_1101-2020_10_26_351783 339 1 11 11 CD 10_1101-2020_10_26_351783 339 2 . . . 10_1101-2020_10_26_351783 340 1 Langfelder Langfelder NNP 10_1101-2020_10_26_351783 340 2 P P NNP 10_1101-2020_10_26_351783 340 3 , , , 10_1101-2020_10_26_351783 340 4 Horvath Horvath NNP 10_1101-2020_10_26_351783 340 5 S. S. NNP 10_1101-2020_10_26_351783 340 6 WGCNA WGCNA NNP 10_1101-2020_10_26_351783 340 7 : : : 10_1101-2020_10_26_351783 340 8 An an DT 10_1101-2020_10_26_351783 340 9 R r NN 10_1101-2020_10_26_351783 340 10 package package NN 10_1101-2020_10_26_351783 340 11 for for IN 10_1101-2020_10_26_351783 340 12 weighted weighted JJ 10_1101-2020_10_26_351783 340 13 correlation correlation NN 10_1101-2020_10_26_351783 340 14 network network NN 10_1101-2020_10_26_351783 340 15 analysis analysis NN 10_1101-2020_10_26_351783 340 16 . . . 10_1101-2020_10_26_351783 341 1 BMC BMC NNP 10_1101-2020_10_26_351783 341 2 Bioinformatics Bioinformatics NNP 10_1101-2020_10_26_351783 341 3 . . . 10_1101-2020_10_26_351783 342 1 2008;9 2008;9 LS 10_1101-2020_10_26_351783 342 2 . . . 10_1101-2020_10_26_351783 343 1 12 12 CD 10_1101-2020_10_26_351783 343 2 . . . 10_1101-2020_10_26_351783 344 1 Choobdar Choobdar NNP 10_1101-2020_10_26_351783 344 2 S S NNP 10_1101-2020_10_26_351783 344 3 , , , 10_1101-2020_10_26_351783 344 4 Ahsen Ahsen NNP 10_1101-2020_10_26_351783 344 5 ME ME NNP 10_1101-2020_10_26_351783 344 6 , , , 10_1101-2020_10_26_351783 344 7 Crawford Crawford NNP 10_1101-2020_10_26_351783 344 8 J J NNP 10_1101-2020_10_26_351783 344 9 , , , 10_1101-2020_10_26_351783 344 10 Tomasoni Tomasoni NNP 10_1101-2020_10_26_351783 344 11 M M NNP 10_1101-2020_10_26_351783 344 12 , , , 10_1101-2020_10_26_351783 344 13 Fang Fang NNP 10_1101-2020_10_26_351783 344 14 T T NNP 10_1101-2020_10_26_351783 344 15 , , , 10_1101-2020_10_26_351783 344 16 Lamparter Lamparter NNP 10_1101-2020_10_26_351783 344 17 D D NNP 10_1101-2020_10_26_351783 344 18 , , , 10_1101-2020_10_26_351783 344 19 et et NNP 10_1101-2020_10_26_351783 344 20 al al NNP 10_1101-2020_10_26_351783 344 21 . . . 10_1101-2020_10_26_351783 345 1 Assessment assessment NN 10_1101-2020_10_26_351783 345 2 of of IN 10_1101-2020_10_26_351783 345 3 network network NN 10_1101-2020_10_26_351783 345 4 module module JJ 10_1101-2020_10_26_351783 345 5 identification identification NN 10_1101-2020_10_26_351783 345 6 across across IN 10_1101-2020_10_26_351783 345 7 complex complex JJ 10_1101-2020_10_26_351783 345 8 diseases disease NNS 10_1101-2020_10_26_351783 345 9 . . . 10_1101-2020_10_26_351783 346 1 Nat Nat NNP 10_1101-2020_10_26_351783 346 2 Methods Methods NNP 10_1101-2020_10_26_351783 346 3 . . . 10_1101-2020_10_26_351783 347 1 2019;16:843–52 2019;16:843–52 NNP 10_1101-2020_10_26_351783 347 2 . . . 10_1101-2020_10_26_351783 348 1 13 13 CD 10_1101-2020_10_26_351783 348 2 . . . 10_1101-2020_10_26_351783 348 3 de de NNP 10_1101-2020_10_26_351783 348 4 Weerd Weerd NNP 10_1101-2020_10_26_351783 348 5 HA HA NNP 10_1101-2020_10_26_351783 348 6 , , , 10_1101-2020_10_26_351783 348 7 Badam Badam NNP 10_1101-2020_10_26_351783 348 8 TVS TVS NNP 10_1101-2020_10_26_351783 348 9 , , , 10_1101-2020_10_26_351783 348 10 Martínez Martínez NNP 10_1101-2020_10_26_351783 348 11 - - HYPH 10_1101-2020_10_26_351783 348 12 Enguita Enguita NNP 10_1101-2020_10_26_351783 348 13 D D NNP 10_1101-2020_10_26_351783 348 14 , , , 10_1101-2020_10_26_351783 348 15 Åkesson Åkesson NNP 10_1101-2020_10_26_351783 348 16 J J NNP 10_1101-2020_10_26_351783 348 17 , , , 10_1101-2020_10_26_351783 348 18 Muthas Muthas NNP 10_1101-2020_10_26_351783 348 19 D D NNP 10_1101-2020_10_26_351783 348 20 , , , 10_1101-2020_10_26_351783 348 21 Gustafsson Gustafsson NNP 10_1101-2020_10_26_351783 348 22 M M NNP 10_1101-2020_10_26_351783 348 23 , , , 10_1101-2020_10_26_351783 348 24 et et NNP 10_1101-2020_10_26_351783 348 25 al al NNP 10_1101-2020_10_26_351783 348 26 . . . 10_1101-2020_10_26_351783 349 1 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 349 2 : : : 10_1101-2020_10_26_351783 349 3 an an DT 10_1101-2020_10_26_351783 349 4 Ensemble Ensemble NNP 10_1101-2020_10_26_351783 349 5 R r NN 10_1101-2020_10_26_351783 349 6 Package package NN 10_1101-2020_10_26_351783 349 7 for for IN 10_1101-2020_10_26_351783 349 8 Inference Inference NNP 10_1101-2020_10_26_351783 349 9 of of IN 10_1101-2020_10_26_351783 349 10 Disease Disease NNP 10_1101-2020_10_26_351783 349 11 Modules Modules NNP 10_1101-2020_10_26_351783 349 12 from from IN 10_1101-2020_10_26_351783 349 13 Transcriptomics Transcriptomics NNP 10_1101-2020_10_26_351783 349 14 Networks Networks NNP 10_1101-2020_10_26_351783 349 15 . . . 10_1101-2020_10_26_351783 350 1 Bioinformatics bioinformatic NNS 10_1101-2020_10_26_351783 350 2 . . . 10_1101-2020_10_26_351783 351 1 2020;1–2 2020;1–2 LS 10_1101-2020_10_26_351783 351 2 . . . 10_1101-2020_10_26_351783 352 1 14 14 CD 10_1101-2020_10_26_351783 352 2 . . . 10_1101-2020_10_26_351783 353 1 Tian Tian NNP 10_1101-2020_10_26_351783 353 2 Y Y NNP 10_1101-2020_10_26_351783 353 3 , , , 10_1101-2020_10_26_351783 353 4 Morris Morris NNP 10_1101-2020_10_26_351783 353 5 TJ TJ NNP 10_1101-2020_10_26_351783 353 6 , , , 10_1101-2020_10_26_351783 353 7 Webster Webster NNP 10_1101-2020_10_26_351783 353 8 AP AP NNP 10_1101-2020_10_26_351783 353 9 , , , 10_1101-2020_10_26_351783 353 10 Yang Yang NNP 10_1101-2020_10_26_351783 353 11 Z Z NNP 10_1101-2020_10_26_351783 353 12 , , , 10_1101-2020_10_26_351783 353 13 Beck Beck NNP 10_1101-2020_10_26_351783 353 14 S S NNP 10_1101-2020_10_26_351783 353 15 , , , 10_1101-2020_10_26_351783 353 16 Feber Feber NNP 10_1101-2020_10_26_351783 353 17 A A NNP 10_1101-2020_10_26_351783 353 18 , , , 10_1101-2020_10_26_351783 353 19 et et NNP 10_1101-2020_10_26_351783 353 20 al al NNP 10_1101-2020_10_26_351783 353 21 . . . 10_1101-2020_10_26_351783 354 1 Genome genome JJ 10_1101-2020_10_26_351783 354 2 analysis analysis NN 10_1101-2020_10_26_351783 354 3 ChAMP champ NN 10_1101-2020_10_26_351783 354 4 [ [ -LRB- 10_1101-2020_10_26_351783 354 5 : : : 10_1101-2020_10_26_351783 354 6 updated update VBN 10_1101-2020_10_26_351783 354 7 methylation methylation NN 10_1101-2020_10_26_351783 354 8 analysis analysis NN 10_1101-2020_10_26_351783 354 9 pipeline pipeline NN 10_1101-2020_10_26_351783 354 10 for for IN 10_1101-2020_10_26_351783 354 11 Illumina Illumina NNP 10_1101-2020_10_26_351783 354 12 BeadChips BeadChips NNP 10_1101-2020_10_26_351783 354 13 . . . 10_1101-2020_10_26_351783 355 1 2017;33:3982–4 2017;33:3982–4 CD 10_1101-2020_10_26_351783 355 2 . . . 10_1101-2020_10_26_351783 356 1 15 15 CD 10_1101-2020_10_26_351783 356 2 . . . 10_1101-2020_10_26_351783 357 1 Teschendorff Teschendorff NNP 10_1101-2020_10_26_351783 357 2 AE AE NNP 10_1101-2020_10_26_351783 357 3 , , , 10_1101-2020_10_26_351783 357 4 Marabita Marabita NNP 10_1101-2020_10_26_351783 357 5 F F NNP 10_1101-2020_10_26_351783 357 6 , , , 10_1101-2020_10_26_351783 357 7 Lechner Lechner NNP 10_1101-2020_10_26_351783 357 8 M M NNP 10_1101-2020_10_26_351783 357 9 , , , 10_1101-2020_10_26_351783 357 10 Bartlett Bartlett NNP 10_1101-2020_10_26_351783 357 11 T T NNP 10_1101-2020_10_26_351783 357 12 , , , 10_1101-2020_10_26_351783 357 13 Tegner Tegner NNP 10_1101-2020_10_26_351783 357 14 J J NNP 10_1101-2020_10_26_351783 357 15 , , , 10_1101-2020_10_26_351783 357 16 Gomez Gomez NNP 10_1101-2020_10_26_351783 357 17 - - HYPH 10_1101-2020_10_26_351783 357 18 cabrero cabrero NNP 10_1101-2020_10_26_351783 357 19 D D NNP 10_1101-2020_10_26_351783 357 20 , , , 10_1101-2020_10_26_351783 357 21 et et NNP 10_1101-2020_10_26_351783 357 22 al al NNP 10_1101-2020_10_26_351783 357 23 . . . 10_1101-2020_10_26_351783 358 1 Gene gene NN 10_1101-2020_10_26_351783 358 2 expression expression NN 10_1101-2020_10_26_351783 358 3 A a DT 10_1101-2020_10_26_351783 358 4 beta beta NN 10_1101-2020_10_26_351783 358 5 - - HYPH 10_1101-2020_10_26_351783 358 6 mixture mixture NN 10_1101-2020_10_26_351783 358 7 quantile quantile NN 10_1101-2020_10_26_351783 358 8 normalization normalization NN 10_1101-2020_10_26_351783 358 9 method method NN 10_1101-2020_10_26_351783 358 10 for for IN 10_1101-2020_10_26_351783 358 11 correcting correct VBG 10_1101-2020_10_26_351783 358 12 probe probe NN 10_1101-2020_10_26_351783 358 13 design design NN 10_1101-2020_10_26_351783 358 14 bias bias NN 10_1101-2020_10_26_351783 358 15 in in IN 10_1101-2020_10_26_351783 358 16 Illumina Illumina NNP 10_1101-2020_10_26_351783 358 17 Infinium Infinium NNP 10_1101-2020_10_26_351783 358 18 450 450 CD 10_1101-2020_10_26_351783 358 19 k k NN 10_1101-2020_10_26_351783 358 20 DNA dna NN 10_1101-2020_10_26_351783 358 21 methylation methylation NN 10_1101-2020_10_26_351783 358 22 data datum NNS 10_1101-2020_10_26_351783 358 23 . . . 10_1101-2020_10_26_351783 359 1 2013;29:189–96 2013;29:189–96 CD 10_1101-2020_10_26_351783 359 2 . . . 10_1101-2020_10_26_351783 360 1 16 16 CD 10_1101-2020_10_26_351783 360 2 . . . 10_1101-2020_10_26_351783 361 1 Johnson Johnson NNP 10_1101-2020_10_26_351783 361 2 WE WE NNP 10_1101-2020_10_26_351783 361 3 , , , 10_1101-2020_10_26_351783 361 4 Li Li NNP 10_1101-2020_10_26_351783 361 5 C. C. NNP 10_1101-2020_10_26_351783 361 6 Adjusting Adjusting NNP 10_1101-2020_10_26_351783 361 7 batch batch NN 10_1101-2020_10_26_351783 361 8 effects effect NNS 10_1101-2020_10_26_351783 361 9 in in IN 10_1101-2020_10_26_351783 361 10 microarray microarray JJ 10_1101-2020_10_26_351783 361 11 expression expression NN 10_1101-2020_10_26_351783 361 12 data datum NNS 10_1101-2020_10_26_351783 361 13 using use VBG 10_1101-2020_10_26_351783 361 14 empirical empirical JJ 10_1101-2020_10_26_351783 361 15 Bayes Bayes NNP 10_1101-2020_10_26_351783 361 16 methods method NNS 10_1101-2020_10_26_351783 361 17 . . . 10_1101-2020_10_26_351783 362 1 2007;118–27 2007;118–27 NN 10_1101-2020_10_26_351783 362 2 . . . 10_1101-2020_10_26_351783 363 1 17 17 CD 10_1101-2020_10_26_351783 363 2 . . . 10_1101-2020_10_26_351783 364 1 Ritchie Ritchie NNP 10_1101-2020_10_26_351783 364 2 ME ME NNP 10_1101-2020_10_26_351783 364 3 , , , 10_1101-2020_10_26_351783 364 4 Phipson Phipson NNP 10_1101-2020_10_26_351783 364 5 B B NNP 10_1101-2020_10_26_351783 364 6 , , , 10_1101-2020_10_26_351783 364 7 Wu Wu NNP 10_1101-2020_10_26_351783 364 8 D D NNP 10_1101-2020_10_26_351783 364 9 , , , 10_1101-2020_10_26_351783 364 10 Hu Hu NNP 10_1101-2020_10_26_351783 364 11 Y Y NNP 10_1101-2020_10_26_351783 364 12 , , , 10_1101-2020_10_26_351783 364 13 Law Law NNP 10_1101-2020_10_26_351783 364 14 CW CW NNP 10_1101-2020_10_26_351783 364 15 , , , 10_1101-2020_10_26_351783 364 16 Shi Shi NNP 10_1101-2020_10_26_351783 364 17 W W NNP 10_1101-2020_10_26_351783 364 18 , , , 10_1101-2020_10_26_351783 364 19 et et NNP 10_1101-2020_10_26_351783 364 20 al al NNP 10_1101-2020_10_26_351783 364 21 . . . 10_1101-2020_10_26_351783 365 1 limma limma NNP 10_1101-2020_10_26_351783 365 2 powers powers NNP 10_1101-2020_10_26_351783 365 3 differential differential VBP 10_1101-2020_10_26_351783 365 4 expression expression NN 10_1101-2020_10_26_351783 365 5 analyses analysis NNS 10_1101-2020_10_26_351783 365 6 for for IN 10_1101-2020_10_26_351783 365 7 RNA RNA NNP 10_1101-2020_10_26_351783 365 8 - - HYPH 10_1101-2020_10_26_351783 365 9 sequencing sequencing NN 10_1101-2020_10_26_351783 365 10 and and CC 10_1101-2020_10_26_351783 365 11 microarray microarray JJ 10_1101-2020_10_26_351783 365 12 studies study NNS 10_1101-2020_10_26_351783 365 13 . . . 10_1101-2020_10_26_351783 366 1 2015;43 2015;43 NNP 10_1101-2020_10_26_351783 366 2 . . . 10_1101-2020_10_26_351783 367 1 ( ( -LRB- 10_1101-2020_10_26_351783 367 2 which which WDT 10_1101-2020_10_26_351783 367 3 was be VBD 10_1101-2020_10_26_351783 367 4 not not RB 10_1101-2020_10_26_351783 367 5 certified certify VBN 10_1101-2020_10_26_351783 367 6 by by IN 10_1101-2020_10_26_351783 367 7 peer peer NN 10_1101-2020_10_26_351783 367 8 review review NN 10_1101-2020_10_26_351783 367 9 ) ) -RRB- 10_1101-2020_10_26_351783 367 10 is be VBZ 10_1101-2020_10_26_351783 367 11 the the DT 10_1101-2020_10_26_351783 367 12 author author NN 10_1101-2020_10_26_351783 367 13 / / SYM 10_1101-2020_10_26_351783 367 14 funder funder NN 10_1101-2020_10_26_351783 367 15 . . . 10_1101-2020_10_26_351783 368 1 All all DT 10_1101-2020_10_26_351783 368 2 rights right NNS 10_1101-2020_10_26_351783 368 3 reserved reserve VBD 10_1101-2020_10_26_351783 368 4 . . . 10_1101-2020_10_26_351783 369 1 No no DT 10_1101-2020_10_26_351783 369 2 reuse reuse NN 10_1101-2020_10_26_351783 369 3 allowed allow VBN 10_1101-2020_10_26_351783 369 4 without without IN 10_1101-2020_10_26_351783 369 5 permission permission NN 10_1101-2020_10_26_351783 369 6 . . . 10_1101-2020_10_26_351783 370 1 The the DT 10_1101-2020_10_26_351783 370 2 copyright copyright NN 10_1101-2020_10_26_351783 370 3 holder holder NN 10_1101-2020_10_26_351783 370 4 for for IN 10_1101-2020_10_26_351783 370 5 this this DT 10_1101-2020_10_26_351783 370 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 370 7 version version NN 10_1101-2020_10_26_351783 370 8 posted post VBD 10_1101-2020_10_26_351783 370 9 January January NNP 10_1101-2020_10_26_351783 370 10 6 6 CD 10_1101-2020_10_26_351783 370 11 , , , 10_1101-2020_10_26_351783 370 12 2021 2021 CD 10_1101-2020_10_26_351783 370 13 . . . 10_1101-2020_10_26_351783 370 14 ; ; : 10_1101-2020_10_26_351783 370 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 370 16 : : : 10_1101-2020_10_26_351783 370 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 370 18 preprint preprint NN 10_1101-2020_10_26_351783 370 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 370 20 22 22 CD 10_1101-2020_10_26_351783 370 21 18 18 CD 10_1101-2020_10_26_351783 370 22 . . . 10_1101-2020_10_26_351783 371 1 Lamparter lamparter NN 10_1101-2020_10_26_351783 371 2 D d NN 10_1101-2020_10_26_351783 371 3 , , , 10_1101-2020_10_26_351783 371 4 Marbach Marbach NNP 10_1101-2020_10_26_351783 371 5 D D NNP 10_1101-2020_10_26_351783 371 6 , , , 10_1101-2020_10_26_351783 371 7 Rueedi Rueedi NNP 10_1101-2020_10_26_351783 371 8 R R NNP 10_1101-2020_10_26_351783 371 9 , , , 10_1101-2020_10_26_351783 371 10 Kutalik Kutalik NNP 10_1101-2020_10_26_351783 371 11 Z Z NNP 10_1101-2020_10_26_351783 371 12 , , , 10_1101-2020_10_26_351783 371 13 Bergmann Bergmann NNP 10_1101-2020_10_26_351783 371 14 S. S. NNP 10_1101-2020_10_26_351783 371 15 Fast Fast NNP 10_1101-2020_10_26_351783 371 16 and and CC 10_1101-2020_10_26_351783 371 17 Rigorous rigorous JJ 10_1101-2020_10_26_351783 371 18 Computation Computation NNP 10_1101-2020_10_26_351783 371 19 of of IN 10_1101-2020_10_26_351783 371 20 Gene Gene NNP 10_1101-2020_10_26_351783 371 21 and and CC 10_1101-2020_10_26_351783 371 22 Pathway Pathway NNP 10_1101-2020_10_26_351783 371 23 Scores Scores NNPS 10_1101-2020_10_26_351783 371 24 from from IN 10_1101-2020_10_26_351783 371 25 SNP SNP NNP 10_1101-2020_10_26_351783 371 26 - - HYPH 10_1101-2020_10_26_351783 371 27 Based Based NNP 10_1101-2020_10_26_351783 371 28 Summary Summary NNP 10_1101-2020_10_26_351783 371 29 Statistics Statistics NNPS 10_1101-2020_10_26_351783 371 30 . . . 10_1101-2020_10_26_351783 372 1 PLoS PLoS : 10_1101-2020_10_26_351783 372 2 Comput Comput NNP 10_1101-2020_10_26_351783 372 3 Biol Biol NNP 10_1101-2020_10_26_351783 372 4 . . . 10_1101-2020_10_26_351783 373 1 2016;12:1–20 2016;12:1–20 LS 10_1101-2020_10_26_351783 373 2 . . . 10_1101-2020_10_26_351783 374 1 19 19 CD 10_1101-2020_10_26_351783 374 2 . . . 10_1101-2020_10_26_351783 375 1 Mosteller Mosteller NNP 10_1101-2020_10_26_351783 375 2 , , , 10_1101-2020_10_26_351783 375 3 F. F. NNP 10_1101-2020_10_26_351783 375 4 and and CC 10_1101-2020_10_26_351783 375 5 Fisher Fisher NNP 10_1101-2020_10_26_351783 375 6 R. R. NNP 10_1101-2020_10_26_351783 375 7 A. A. NNP 10_1101-2020_10_26_351783 376 1 Questions question NNS 10_1101-2020_10_26_351783 376 2 and and CC 10_1101-2020_10_26_351783 376 3 Answers answer NNS 10_1101-2020_10_26_351783 376 4 # # $ 10_1101-2020_10_26_351783 376 5 14 14 CD 10_1101-2020_10_26_351783 376 6 Author author NN 10_1101-2020_10_26_351783 376 7 ( ( -LRB- 10_1101-2020_10_26_351783 376 8 s s NN 10_1101-2020_10_26_351783 376 9 ): ): NN 10_1101-2020_10_26_351783 376 10 Frederick Frederick NNP 10_1101-2020_10_26_351783 376 11 Mosteller Mosteller NNP 10_1101-2020_10_26_351783 376 12 and and CC 10_1101-2020_10_26_351783 376 13 R r NN 10_1101-2020_10_26_351783 376 14 . . . 10_1101-2020_10_26_351783 377 1 A a DT 10_1101-2020_10_26_351783 377 2 . . . 10_1101-2020_10_26_351783 378 1 Fisher Fisher NNP 10_1101-2020_10_26_351783 378 2 Published publish VBN 10_1101-2020_10_26_351783 378 3 by by IN 10_1101-2020_10_26_351783 378 4 [ [ -LRB- 10_1101-2020_10_26_351783 378 5 : : : 10_1101-2020_10_26_351783 378 6 Taylor Taylor NNP 10_1101-2020_10_26_351783 378 7 & & CC 10_1101-2020_10_26_351783 378 8 Francis Francis NNP 10_1101-2020_10_26_351783 378 9 , , , 10_1101-2020_10_26_351783 378 10 Ltd Ltd NNP 10_1101-2020_10_26_351783 378 11 . . . 10_1101-2020_10_26_351783 379 1 on on IN 10_1101-2020_10_26_351783 379 2 behalf behalf NN 10_1101-2020_10_26_351783 379 3 of of IN 10_1101-2020_10_26_351783 379 4 the the DT 10_1101-2020_10_26_351783 379 5 American American NNP 10_1101-2020_10_26_351783 379 6 Statistical Statistical NNP 10_1101-2020_10_26_351783 379 7 Association Association NNP 10_1101-2020_10_26_351783 379 8 Stable Stable NNP 10_1101-2020_10_26_351783 379 9 URL URL NNP 10_1101-2020_10_26_351783 379 10 [ [ -LRB- 10_1101-2020_10_26_351783 379 11 : : : 10_1101-2020_10_26_351783 379 12 http://www.jstor.org/stable/2681650 http://www.jstor.org/stable/2681650 VBG 10_1101-2020_10_26_351783 379 13 All all DT 10_1101-2020_10_26_351783 379 14 use use NN 10_1101-2020_10_26_351783 379 15 subject subject JJ 10_1101-2020_10_26_351783 379 16 to to IN 10_1101-2020_10_26_351783 379 17 http://about.jsto http://about.jsto NNP 10_1101-2020_10_26_351783 379 18 . . . 10_1101-2020_10_26_351783 380 1 1948;2:30–1 1948;2:30–1 CD 10_1101-2020_10_26_351783 380 2 . . . 10_1101-2020_10_26_351783 381 1 Available available JJ 10_1101-2020_10_26_351783 381 2 from from IN 10_1101-2020_10_26_351783 381 3 : : : 10_1101-2020_10_26_351783 381 4 http://www.jstor.org/stable/2681650 http://www.jstor.org/stable/2681650 VBG 10_1101-2020_10_26_351783 381 5 20 20 CD 10_1101-2020_10_26_351783 381 6 . . . 10_1101-2020_10_26_351783 382 1 Piñero Piñero NNP 10_1101-2020_10_26_351783 382 2 J J NNP 10_1101-2020_10_26_351783 382 3 , , , 10_1101-2020_10_26_351783 382 4 Ramírez Ramírez NNP 10_1101-2020_10_26_351783 382 5 - - HYPH 10_1101-2020_10_26_351783 382 6 Anguita Anguita NNP 10_1101-2020_10_26_351783 382 7 JM JM NNP 10_1101-2020_10_26_351783 382 8 , , , 10_1101-2020_10_26_351783 382 9 Saüch Saüch NNP 10_1101-2020_10_26_351783 382 10 - - HYPH 10_1101-2020_10_26_351783 382 11 Pitarch Pitarch NNP 10_1101-2020_10_26_351783 382 12 J J NNP 10_1101-2020_10_26_351783 382 13 , , , 10_1101-2020_10_26_351783 382 14 Ronzano Ronzano NNP 10_1101-2020_10_26_351783 382 15 F F NNP 10_1101-2020_10_26_351783 382 16 , , , 10_1101-2020_10_26_351783 382 17 Centeno Centeno NNP 10_1101-2020_10_26_351783 382 18 E E NNP 10_1101-2020_10_26_351783 382 19 , , , 10_1101-2020_10_26_351783 382 20 Sanz Sanz NNP 10_1101-2020_10_26_351783 382 21 F F NNP 10_1101-2020_10_26_351783 382 22 , , , 10_1101-2020_10_26_351783 382 23 et et NNP 10_1101-2020_10_26_351783 382 24 al al NNP 10_1101-2020_10_26_351783 382 25 . . . 10_1101-2020_10_26_351783 383 1 The the DT 10_1101-2020_10_26_351783 383 2 DisGeNET DisGeNET NNP 10_1101-2020_10_26_351783 383 3 knowledge knowledge NN 10_1101-2020_10_26_351783 383 4 platform platform NN 10_1101-2020_10_26_351783 383 5 for for IN 10_1101-2020_10_26_351783 383 6 disease disease NNP 10_1101-2020_10_26_351783 383 7 genomics genomic NNS 10_1101-2020_10_26_351783 383 8 : : : 10_1101-2020_10_26_351783 383 9 2019 2019 CD 10_1101-2020_10_26_351783 383 10 update update NN 10_1101-2020_10_26_351783 383 11 . . . 10_1101-2020_10_26_351783 384 1 Nucleic Nucleic NNP 10_1101-2020_10_26_351783 384 2 Acids Acids NNPS 10_1101-2020_10_26_351783 384 3 Res Res NNP 10_1101-2020_10_26_351783 384 4 . . . 10_1101-2020_10_26_351783 385 1 2020;48 2020;48 UH 10_1101-2020_10_26_351783 385 2 : : : 10_1101-2020_10_26_351783 385 3 D845–55 D845–55 NNP 10_1101-2020_10_26_351783 385 4 . . . 10_1101-2020_10_26_351783 386 1 21 21 CD 10_1101-2020_10_26_351783 386 2 . . . 10_1101-2020_10_26_351783 387 1 Yu Yu NNP 10_1101-2020_10_26_351783 387 2 G G NNP 10_1101-2020_10_26_351783 387 3 , , , 10_1101-2020_10_26_351783 387 4 Wang Wang NNP 10_1101-2020_10_26_351783 387 5 LG LG NNP 10_1101-2020_10_26_351783 387 6 , , , 10_1101-2020_10_26_351783 387 7 Han Han NNP 10_1101-2020_10_26_351783 387 8 Y Y NNP 10_1101-2020_10_26_351783 387 9 , , , 10_1101-2020_10_26_351783 387 10 He -PRON- PRP 10_1101-2020_10_26_351783 387 11 QY QY NNP 10_1101-2020_10_26_351783 387 12 . . . 10_1101-2020_10_26_351783 388 1 ClusterProfiler ClusterProfiler NNP 10_1101-2020_10_26_351783 388 2 : : : 10_1101-2020_10_26_351783 388 3 An an DT 10_1101-2020_10_26_351783 388 4 R r NN 10_1101-2020_10_26_351783 388 5 package package NN 10_1101-2020_10_26_351783 388 6 for for IN 10_1101-2020_10_26_351783 388 7 comparing compare VBG 10_1101-2020_10_26_351783 388 8 biological biological JJ 10_1101-2020_10_26_351783 388 9 themes theme NNS 10_1101-2020_10_26_351783 388 10 among among IN 10_1101-2020_10_26_351783 388 11 gene gene NN 10_1101-2020_10_26_351783 388 12 clusters cluster NNS 10_1101-2020_10_26_351783 388 13 . . . 10_1101-2020_10_26_351783 389 1 Omi Omi NNP 10_1101-2020_10_26_351783 389 2 A a DT 10_1101-2020_10_26_351783 389 3 J J NNP 10_1101-2020_10_26_351783 389 4 Integr Integr NNP 10_1101-2020_10_26_351783 389 5 Biol Biol NNP 10_1101-2020_10_26_351783 389 6 . . . 10_1101-2020_10_26_351783 390 1 2012;16:284–7 2012;16:284–7 CD 10_1101-2020_10_26_351783 390 2 . . . 10_1101-2020_10_26_351783 391 1 22 22 CD 10_1101-2020_10_26_351783 391 2 . . . 10_1101-2020_10_26_351783 392 1 Paul Paul NNP 10_1101-2020_10_26_351783 392 2 Shannon Shannon NNP 10_1101-2020_10_26_351783 392 3 , , , 10_1101-2020_10_26_351783 392 4 Andrew Andrew NNP 10_1101-2020_10_26_351783 392 5 Markiel Markiel NNP 10_1101-2020_10_26_351783 392 6 , , , 10_1101-2020_10_26_351783 392 7 Owen Owen NNP 10_1101-2020_10_26_351783 392 8 Ozier ozier RBR 10_1101-2020_10_26_351783 392 9 , , , 10_1101-2020_10_26_351783 392 10 Nitin Nitin NNP 10_1101-2020_10_26_351783 392 11 S. S. NNP 10_1101-2020_10_26_351783 392 12 Baliga Baliga NNP 10_1101-2020_10_26_351783 392 13 , , , 10_1101-2020_10_26_351783 392 14 Jonathan Jonathan NNP 10_1101-2020_10_26_351783 392 15 T. T. NNP 10_1101-2020_10_26_351783 392 16 Wang Wang NNP 10_1101-2020_10_26_351783 392 17 , , , 10_1101-2020_10_26_351783 392 18 Daniel Daniel NNP 10_1101-2020_10_26_351783 392 19 Ramage Ramage NNP 10_1101-2020_10_26_351783 392 20 , , , 10_1101-2020_10_26_351783 392 21 Nada Nada NNP 10_1101-2020_10_26_351783 392 22 Amin Amin NNP 10_1101-2020_10_26_351783 392 23 , , , 10_1101-2020_10_26_351783 392 24 Benno Benno NNP 10_1101-2020_10_26_351783 392 25 Schwikowski Schwikowski NNP 10_1101-2020_10_26_351783 392 26 , , , 10_1101-2020_10_26_351783 392 27 and and CC 10_1101-2020_10_26_351783 392 28 Trey Trey NNP 10_1101-2020_10_26_351783 392 29 Ideker Ideker NNP 10_1101-2020_10_26_351783 392 30 . . . 10_1101-2020_10_26_351783 393 1 Cytoscape cytoscape NN 10_1101-2020_10_26_351783 393 2 : : : 10_1101-2020_10_26_351783 393 3 A a DT 10_1101-2020_10_26_351783 393 4 Software Software NNP 10_1101-2020_10_26_351783 393 5 Environment Environment NNP 10_1101-2020_10_26_351783 393 6 for for IN 10_1101-2020_10_26_351783 393 7 Integrated Integrated NNP 10_1101-2020_10_26_351783 393 8 Models Models NNPS 10_1101-2020_10_26_351783 393 9 . . . 10_1101-2020_10_26_351783 394 1 Genome genome JJ 10_1101-2020_10_26_351783 394 2 Res res NN 10_1101-2020_10_26_351783 394 3 [ [ -LRB- 10_1101-2020_10_26_351783 394 4 Internet internet NN 10_1101-2020_10_26_351783 394 5 ] ] -RRB- 10_1101-2020_10_26_351783 394 6 . . . 10_1101-2020_10_26_351783 395 1 1971;13:426 1971;13:426 CD 10_1101-2020_10_26_351783 395 2 . . . 10_1101-2020_10_26_351783 396 1 Available available JJ 10_1101-2020_10_26_351783 396 2 from from IN 10_1101-2020_10_26_351783 396 3 : : : 10_1101-2020_10_26_351783 396 4 http://ci.nii.ac.jp/naid/110001910481/ http://ci.nii.ac.jp/naid/110001910481/ NN 10_1101-2020_10_26_351783 396 5 23 23 CD 10_1101-2020_10_26_351783 396 6 . . . 10_1101-2020_10_26_351783 397 1 Maere Maere NNP 10_1101-2020_10_26_351783 397 2 S S NNP 10_1101-2020_10_26_351783 397 3 , , , 10_1101-2020_10_26_351783 397 4 Heymans Heymans NNPS 10_1101-2020_10_26_351783 397 5 K K NNP 10_1101-2020_10_26_351783 397 6 , , , 10_1101-2020_10_26_351783 397 7 Kuiper Kuiper NNP 10_1101-2020_10_26_351783 397 8 M. M. NNP 10_1101-2020_10_26_351783 397 9 Systems Systems NNP 10_1101-2020_10_26_351783 397 10 biology biology NN 10_1101-2020_10_26_351783 397 11 BiNGO BiNGO NNP 10_1101-2020_10_26_351783 397 12 [ [ -LRB- 10_1101-2020_10_26_351783 397 13 : : : 10_1101-2020_10_26_351783 397 14 a a DT 10_1101-2020_10_26_351783 397 15 Cytoscape Cytoscape NNP 10_1101-2020_10_26_351783 397 16 plugin plugin NN 10_1101-2020_10_26_351783 397 17 to to TO 10_1101-2020_10_26_351783 397 18 assess assess VB 10_1101-2020_10_26_351783 397 19 overrepresentation overrepresentation NN 10_1101-2020_10_26_351783 397 20 of of IN 10_1101-2020_10_26_351783 397 21 Gene Gene NNP 10_1101-2020_10_26_351783 397 22 Ontology Ontology NNP 10_1101-2020_10_26_351783 397 23 categories category NNS 10_1101-2020_10_26_351783 397 24 in in IN 10_1101-2020_10_26_351783 397 25 Biological Biological NNP 10_1101-2020_10_26_351783 397 26 Networks Networks NNP 10_1101-2020_10_26_351783 397 27 . . . 10_1101-2020_10_26_351783 398 1 2005;21:3448–9 2005;21:3448–9 CD 10_1101-2020_10_26_351783 398 2 . . . 10_1101-2020_10_26_351783 399 1 24 24 CD 10_1101-2020_10_26_351783 399 2 . . . 10_1101-2020_10_26_351783 400 1 Supek Supek NNP 10_1101-2020_10_26_351783 400 2 F F NNP 10_1101-2020_10_26_351783 400 3 , , , 10_1101-2020_10_26_351783 400 4 Bošnjak Bošnjak NNP 10_1101-2020_10_26_351783 400 5 M M NNP 10_1101-2020_10_26_351783 400 6 , , , 10_1101-2020_10_26_351783 400 7 Škunca Škunca NNP 10_1101-2020_10_26_351783 400 8 N N NNP 10_1101-2020_10_26_351783 400 9 , , , 10_1101-2020_10_26_351783 400 10 Šmuc Šmuc NNP 10_1101-2020_10_26_351783 400 11 T. T. NNP 10_1101-2020_10_26_351783 400 12 Revigo Revigo NNP 10_1101-2020_10_26_351783 400 13 summarizes summarize VBZ 10_1101-2020_10_26_351783 400 14 and and CC 10_1101-2020_10_26_351783 400 15 visualizes visualize VBZ 10_1101-2020_10_26_351783 400 16 long long JJ 10_1101-2020_10_26_351783 400 17 lists list NNS 10_1101-2020_10_26_351783 400 18 of of IN 10_1101-2020_10_26_351783 400 19 gene gene NN 10_1101-2020_10_26_351783 400 20 ontology ontology NN 10_1101-2020_10_26_351783 400 21 terms term NNS 10_1101-2020_10_26_351783 400 22 . . . 10_1101-2020_10_26_351783 401 1 PLoS PLoS : 10_1101-2020_10_26_351783 401 2 One one CD 10_1101-2020_10_26_351783 401 3 . . . 10_1101-2020_10_26_351783 402 1 2011;6 2011;6 LS 10_1101-2020_10_26_351783 402 2 . . . 10_1101-2020_10_26_351783 403 1 25 25 CD 10_1101-2020_10_26_351783 403 2 . . . 10_1101-2020_10_26_351783 404 1 Carbone Carbone NNP 10_1101-2020_10_26_351783 404 2 F F NNP 10_1101-2020_10_26_351783 404 3 , , , 10_1101-2020_10_26_351783 404 4 De De NNP 10_1101-2020_10_26_351783 404 5 Rosa Rosa NNP 10_1101-2020_10_26_351783 404 6 V V NNP 10_1101-2020_10_26_351783 404 7 , , , 10_1101-2020_10_26_351783 404 8 Carrieri Carrieri NNP 10_1101-2020_10_26_351783 404 9 PB PB NNP 10_1101-2020_10_26_351783 404 10 , , , 10_1101-2020_10_26_351783 404 11 Montella Montella NNP 10_1101-2020_10_26_351783 404 12 S S NNP 10_1101-2020_10_26_351783 404 13 , , , 10_1101-2020_10_26_351783 404 14 Bruzzese Bruzzese NNP 10_1101-2020_10_26_351783 404 15 D d NN 10_1101-2020_10_26_351783 404 16 , , , 10_1101-2020_10_26_351783 404 17 Porcellini Porcellini NNP 10_1101-2020_10_26_351783 404 18 A A NNP 10_1101-2020_10_26_351783 404 19 , , , 10_1101-2020_10_26_351783 404 20 et et NNP 10_1101-2020_10_26_351783 404 21 al al NNP 10_1101-2020_10_26_351783 404 22 . . . 10_1101-2020_10_26_351783 405 1 Regulatory regulatory JJ 10_1101-2020_10_26_351783 405 2 T T NNP 10_1101-2020_10_26_351783 405 3 cell cell NN 10_1101-2020_10_26_351783 405 4 proliferative proliferative JJ 10_1101-2020_10_26_351783 405 5 potential potential NN 10_1101-2020_10_26_351783 405 6 is be VBZ 10_1101-2020_10_26_351783 405 7 impaired impair VBN 10_1101-2020_10_26_351783 405 8 in in IN 10_1101-2020_10_26_351783 405 9 human human JJ 10_1101-2020_10_26_351783 405 10 autoimmune autoimmune JJ 10_1101-2020_10_26_351783 405 11 disease disease NN 10_1101-2020_10_26_351783 405 12 . . . 10_1101-2020_10_26_351783 406 1 Nat Nat NNP 10_1101-2020_10_26_351783 406 2 Med Med NNP 10_1101-2020_10_26_351783 406 3 . . . 10_1101-2020_10_26_351783 407 1 2014;20:69–74 2014;20:69–74 CD 10_1101-2020_10_26_351783 407 2 . . . 10_1101-2020_10_26_351783 408 1 26 26 CD 10_1101-2020_10_26_351783 408 2 . . . 10_1101-2020_10_26_351783 409 1 Mammana Mammana NNP 10_1101-2020_10_26_351783 409 2 S S NNP 10_1101-2020_10_26_351783 409 3 , , , 10_1101-2020_10_26_351783 409 4 Bramanti Bramanti NNP 10_1101-2020_10_26_351783 409 5 P P NNP 10_1101-2020_10_26_351783 409 6 , , , 10_1101-2020_10_26_351783 409 7 Mazzon Mazzon NNP 10_1101-2020_10_26_351783 409 8 E E NNP 10_1101-2020_10_26_351783 409 9 , , , 10_1101-2020_10_26_351783 409 10 Cavalli Cavalli NNP 10_1101-2020_10_26_351783 409 11 E E NNP 10_1101-2020_10_26_351783 409 12 , , , 10_1101-2020_10_26_351783 409 13 Basile Basile NNP 10_1101-2020_10_26_351783 409 14 MS MS NNP 10_1101-2020_10_26_351783 409 15 , , , 10_1101-2020_10_26_351783 409 16 Fagone Fagone NNP 10_1101-2020_10_26_351783 409 17 P P NNP 10_1101-2020_10_26_351783 409 18 , , , 10_1101-2020_10_26_351783 409 19 et et NNP 10_1101-2020_10_26_351783 409 20 al al NNP 10_1101-2020_10_26_351783 409 21 . . . 10_1101-2020_10_26_351783 410 1 Preclinical preclinical JJ 10_1101-2020_10_26_351783 410 2 evaluation evaluation NN 10_1101-2020_10_26_351783 410 3 of of IN 10_1101-2020_10_26_351783 410 4 the the DT 10_1101-2020_10_26_351783 410 5 PI3K PI3K NNP 10_1101-2020_10_26_351783 410 6 / / SYM 10_1101-2020_10_26_351783 410 7 Akt Akt NNP 10_1101-2020_10_26_351783 410 8 / / SYM 10_1101-2020_10_26_351783 410 9 mTOR mtor NN 10_1101-2020_10_26_351783 410 10 pathway pathway NN 10_1101-2020_10_26_351783 410 11 in in IN 10_1101-2020_10_26_351783 410 12 animal animal NN 10_1101-2020_10_26_351783 410 13 models model NNS 10_1101-2020_10_26_351783 410 14 of of IN 10_1101-2020_10_26_351783 410 15 multiple multiple JJ 10_1101-2020_10_26_351783 410 16 sclerosis sclerosis NN 10_1101-2020_10_26_351783 410 17 . . . 10_1101-2020_10_26_351783 411 1 Oncotarget oncotarget RB 10_1101-2020_10_26_351783 411 2 . . . 10_1101-2020_10_26_351783 412 1 2018;9:8263–77 2018;9:8263–77 LS 10_1101-2020_10_26_351783 412 2 . . . 10_1101-2020_10_26_351783 413 1 27 27 CD 10_1101-2020_10_26_351783 413 2 . . . 10_1101-2020_10_26_351783 414 1 Holley Holley NNP 10_1101-2020_10_26_351783 414 2 JE JE NNP 10_1101-2020_10_26_351783 414 3 , , , 10_1101-2020_10_26_351783 414 4 Gveric Gveric NNP 10_1101-2020_10_26_351783 414 5 D D NNP 10_1101-2020_10_26_351783 414 6 , , , 10_1101-2020_10_26_351783 414 7 Newcombe Newcombe NNP 10_1101-2020_10_26_351783 414 8 J J NNP 10_1101-2020_10_26_351783 414 9 , , , 10_1101-2020_10_26_351783 414 10 Cuzner Cuzner NNP 10_1101-2020_10_26_351783 414 11 ML ML NNP 10_1101-2020_10_26_351783 414 12 , , , 10_1101-2020_10_26_351783 414 13 Gutowski Gutowski NNP 10_1101-2020_10_26_351783 414 14 NJ NJ NNP 10_1101-2020_10_26_351783 414 15 . . . 10_1101-2020_10_26_351783 415 1 Astrocyte astrocyte IN 10_1101-2020_10_26_351783 415 2 characterization characterization NN 10_1101-2020_10_26_351783 415 3 in in IN 10_1101-2020_10_26_351783 415 4 the the DT 10_1101-2020_10_26_351783 415 5 ( ( -LRB- 10_1101-2020_10_26_351783 415 6 which which WDT 10_1101-2020_10_26_351783 415 7 was be VBD 10_1101-2020_10_26_351783 415 8 not not RB 10_1101-2020_10_26_351783 415 9 certified certify VBN 10_1101-2020_10_26_351783 415 10 by by IN 10_1101-2020_10_26_351783 415 11 peer peer NN 10_1101-2020_10_26_351783 415 12 review review NN 10_1101-2020_10_26_351783 415 13 ) ) -RRB- 10_1101-2020_10_26_351783 415 14 is be VBZ 10_1101-2020_10_26_351783 415 15 the the DT 10_1101-2020_10_26_351783 415 16 author author NN 10_1101-2020_10_26_351783 415 17 / / SYM 10_1101-2020_10_26_351783 415 18 funder funder NN 10_1101-2020_10_26_351783 415 19 . . . 10_1101-2020_10_26_351783 416 1 All all DT 10_1101-2020_10_26_351783 416 2 rights right NNS 10_1101-2020_10_26_351783 416 3 reserved reserve VBD 10_1101-2020_10_26_351783 416 4 . . . 10_1101-2020_10_26_351783 417 1 No no DT 10_1101-2020_10_26_351783 417 2 reuse reuse NN 10_1101-2020_10_26_351783 417 3 allowed allow VBN 10_1101-2020_10_26_351783 417 4 without without IN 10_1101-2020_10_26_351783 417 5 permission permission NN 10_1101-2020_10_26_351783 417 6 . . . 10_1101-2020_10_26_351783 418 1 The the DT 10_1101-2020_10_26_351783 418 2 copyright copyright NN 10_1101-2020_10_26_351783 418 3 holder holder NN 10_1101-2020_10_26_351783 418 4 for for IN 10_1101-2020_10_26_351783 418 5 this this DT 10_1101-2020_10_26_351783 418 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 418 7 version version NN 10_1101-2020_10_26_351783 418 8 posted post VBD 10_1101-2020_10_26_351783 418 9 January January NNP 10_1101-2020_10_26_351783 418 10 6 6 CD 10_1101-2020_10_26_351783 418 11 , , , 10_1101-2020_10_26_351783 418 12 2021 2021 CD 10_1101-2020_10_26_351783 418 13 . . . 10_1101-2020_10_26_351783 418 14 ; ; : 10_1101-2020_10_26_351783 418 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 418 16 : : : 10_1101-2020_10_26_351783 418 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 418 18 preprint preprint NN 10_1101-2020_10_26_351783 418 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 418 20 23 23 CD 10_1101-2020_10_26_351783 418 21 multiple multiple JJ 10_1101-2020_10_26_351783 418 22 sclerosis sclerosis NN 10_1101-2020_10_26_351783 418 23 glial glial NN 10_1101-2020_10_26_351783 418 24 scar scar NN 10_1101-2020_10_26_351783 418 25 . . . 10_1101-2020_10_26_351783 419 1 Neuropathol Neuropathol NNP 10_1101-2020_10_26_351783 419 2 Appl Appl NNP 10_1101-2020_10_26_351783 419 3 Neurobiol Neurobiol NNP 10_1101-2020_10_26_351783 419 4 . . . 10_1101-2020_10_26_351783 420 1 2003;29:434–44 2003;29:434–44 LS 10_1101-2020_10_26_351783 420 2 . . . 10_1101-2020_10_26_351783 421 1 28 28 CD 10_1101-2020_10_26_351783 421 2 . . . 10_1101-2020_10_26_351783 422 1 Pedotti Pedotti NNP 10_1101-2020_10_26_351783 422 2 R R NNP 10_1101-2020_10_26_351783 422 3 , , , 10_1101-2020_10_26_351783 422 4 DeVoss DeVoss NNP 10_1101-2020_10_26_351783 422 5 JJ JJ NNP 10_1101-2020_10_26_351783 422 6 , , , 10_1101-2020_10_26_351783 422 7 Youssef Youssef NNP 10_1101-2020_10_26_351783 422 8 S S NNP 10_1101-2020_10_26_351783 422 9 , , , 10_1101-2020_10_26_351783 422 10 Mitchell Mitchell NNP 10_1101-2020_10_26_351783 422 11 D D NNP 10_1101-2020_10_26_351783 422 12 , , , 10_1101-2020_10_26_351783 422 13 Wedemeyer Wedemeyer NNP 10_1101-2020_10_26_351783 422 14 J J NNP 10_1101-2020_10_26_351783 422 15 , , , 10_1101-2020_10_26_351783 422 16 Madanat Madanat NNP 10_1101-2020_10_26_351783 422 17 R R NNP 10_1101-2020_10_26_351783 422 18 , , , 10_1101-2020_10_26_351783 422 19 et et NNP 10_1101-2020_10_26_351783 422 20 al al NNP 10_1101-2020_10_26_351783 422 21 . . . 10_1101-2020_10_26_351783 423 1 Multiple multiple JJ 10_1101-2020_10_26_351783 423 2 elements element NNS 10_1101-2020_10_26_351783 423 3 of of IN 10_1101-2020_10_26_351783 423 4 the the DT 10_1101-2020_10_26_351783 423 5 allergic allergic JJ 10_1101-2020_10_26_351783 423 6 arm arm NN 10_1101-2020_10_26_351783 423 7 of of IN 10_1101-2020_10_26_351783 423 8 the the DT 10_1101-2020_10_26_351783 423 9 immune immune JJ 10_1101-2020_10_26_351783 423 10 response response NN 10_1101-2020_10_26_351783 423 11 modulate modulate NNP 10_1101-2020_10_26_351783 423 12 autoimmune autoimmune JJ 10_1101-2020_10_26_351783 423 13 demyelination demyelination NN 10_1101-2020_10_26_351783 423 14 . . . 10_1101-2020_10_26_351783 424 1 Proc Proc NNP 10_1101-2020_10_26_351783 424 2 Natl Natl NNP 10_1101-2020_10_26_351783 424 3 Acad Acad NNP 10_1101-2020_10_26_351783 424 4 Sci Sci NNP 10_1101-2020_10_26_351783 424 5 U U NNP 10_1101-2020_10_26_351783 424 6 S S NNP 10_1101-2020_10_26_351783 424 7 A. a. NN 10_1101-2020_10_26_351783 425 1 2003;100:1867–72 2003;100:1867–72 LS 10_1101-2020_10_26_351783 425 2 . . . 10_1101-2020_10_26_351783 426 1 29 29 CD 10_1101-2020_10_26_351783 426 2 . . . 10_1101-2020_10_26_351783 427 1 Cui Cui NNP 10_1101-2020_10_26_351783 427 2 LY LY NNP 10_1101-2020_10_26_351783 427 3 , , , 10_1101-2020_10_26_351783 427 4 Chu Chu NNP 10_1101-2020_10_26_351783 427 5 SF SF NNP 10_1101-2020_10_26_351783 427 6 , , , 10_1101-2020_10_26_351783 427 7 Chen Chen NNP 10_1101-2020_10_26_351783 427 8 NH NH NNP 10_1101-2020_10_26_351783 427 9 . . . 10_1101-2020_10_26_351783 428 1 The the DT 10_1101-2020_10_26_351783 428 2 role role NN 10_1101-2020_10_26_351783 428 3 of of IN 10_1101-2020_10_26_351783 428 4 chemokines chemokine NNS 10_1101-2020_10_26_351783 428 5 and and CC 10_1101-2020_10_26_351783 428 6 chemokine chemokine NNP 10_1101-2020_10_26_351783 428 7 receptors receptor NNS 10_1101-2020_10_26_351783 428 8 in in IN 10_1101-2020_10_26_351783 428 9 multiple multiple JJ 10_1101-2020_10_26_351783 428 10 sclerosis sclerosis NN 10_1101-2020_10_26_351783 428 11 . . . 10_1101-2020_10_26_351783 429 1 Int Int NNP 10_1101-2020_10_26_351783 429 2 Immunopharmacol Immunopharmacol NNP 10_1101-2020_10_26_351783 429 3 [ [ -LRB- 10_1101-2020_10_26_351783 429 4 Internet internet NN 10_1101-2020_10_26_351783 429 5 ] ] -RRB- 10_1101-2020_10_26_351783 429 6 . . . 10_1101-2020_10_26_351783 430 1 Elsevier elsevier NN 10_1101-2020_10_26_351783 430 2 ; ; : 10_1101-2020_10_26_351783 430 3 2020;83:106314 2020;83:106314 CD 10_1101-2020_10_26_351783 430 4 . . . 10_1101-2020_10_26_351783 431 1 Available available JJ 10_1101-2020_10_26_351783 431 2 from from IN 10_1101-2020_10_26_351783 431 3 : : : 10_1101-2020_10_26_351783 431 4 https://doi.org/10.1016/j.intimp.2020.106314 https://doi.org/10.1016/j.intimp.2020.106314 NNP 10_1101-2020_10_26_351783 431 5 30 30 CD 10_1101-2020_10_26_351783 431 6 . . . 10_1101-2020_10_26_351783 432 1 Krumbholz Krumbholz NNP 10_1101-2020_10_26_351783 432 2 M M NNP 10_1101-2020_10_26_351783 432 3 , , , 10_1101-2020_10_26_351783 432 4 Theil Theil NNP 10_1101-2020_10_26_351783 432 5 D D NNP 10_1101-2020_10_26_351783 432 6 , , , 10_1101-2020_10_26_351783 432 7 Cepok Cepok NNP 10_1101-2020_10_26_351783 432 8 S S NNP 10_1101-2020_10_26_351783 432 9 , , , 10_1101-2020_10_26_351783 432 10 Hemmer Hemmer NNP 10_1101-2020_10_26_351783 432 11 B B NNP 10_1101-2020_10_26_351783 432 12 , , , 10_1101-2020_10_26_351783 432 13 Kivisäkk Kivisäkk NNP 10_1101-2020_10_26_351783 432 14 P P NNP 10_1101-2020_10_26_351783 432 15 , , , 10_1101-2020_10_26_351783 432 16 Ransohoff Ransohoff NNP 10_1101-2020_10_26_351783 432 17 RM RM NNP 10_1101-2020_10_26_351783 432 18 , , , 10_1101-2020_10_26_351783 432 19 et et NNP 10_1101-2020_10_26_351783 432 20 al al NNP 10_1101-2020_10_26_351783 432 21 . . . 10_1101-2020_10_26_351783 433 1 Chemokines chemokine NNS 10_1101-2020_10_26_351783 433 2 in in IN 10_1101-2020_10_26_351783 433 3 multiple multiple JJ 10_1101-2020_10_26_351783 433 4 sclerosis sclerosis NN 10_1101-2020_10_26_351783 433 5 : : : 10_1101-2020_10_26_351783 433 6 CXCL12 cxcl12 NN 10_1101-2020_10_26_351783 433 7 and and CC 10_1101-2020_10_26_351783 433 8 CXCL13 CXCL13 NNP 10_1101-2020_10_26_351783 433 9 up up IN 10_1101-2020_10_26_351783 433 10 - - HYPH 10_1101-2020_10_26_351783 433 11 regulation regulation NN 10_1101-2020_10_26_351783 433 12 is be VBZ 10_1101-2020_10_26_351783 433 13 differentially differentially RB 10_1101-2020_10_26_351783 433 14 linked link VBN 10_1101-2020_10_26_351783 433 15 to to IN 10_1101-2020_10_26_351783 433 16 CNS CNS NNP 10_1101-2020_10_26_351783 433 17 immune immune JJ 10_1101-2020_10_26_351783 433 18 cell cell NN 10_1101-2020_10_26_351783 433 19 recruitment recruitment NN 10_1101-2020_10_26_351783 433 20 . . . 10_1101-2020_10_26_351783 434 1 Brain brain NN 10_1101-2020_10_26_351783 434 2 . . . 10_1101-2020_10_26_351783 435 1 2006;129:200–11 2006;129:200–11 CD 10_1101-2020_10_26_351783 435 2 . . . 10_1101-2020_10_26_351783 436 1 31 31 CD 10_1101-2020_10_26_351783 436 2 . . . 10_1101-2020_10_26_351783 437 1 Krementsov Krementsov NNP 10_1101-2020_10_26_351783 437 2 DN DN NNP 10_1101-2020_10_26_351783 437 3 , , , 10_1101-2020_10_26_351783 437 4 Thornton Thornton NNP 10_1101-2020_10_26_351783 437 5 TM TM NNP 10_1101-2020_10_26_351783 437 6 , , , 10_1101-2020_10_26_351783 437 7 Teuscher Teuscher NNP 10_1101-2020_10_26_351783 437 8 C C NNP 10_1101-2020_10_26_351783 437 9 , , , 10_1101-2020_10_26_351783 437 10 Rincon Rincon NNP 10_1101-2020_10_26_351783 437 11 M. M. NNP 10_1101-2020_10_26_351783 437 12 The The NNP 10_1101-2020_10_26_351783 437 13 Emerging Emerging NNP 10_1101-2020_10_26_351783 437 14 Role Role NNP 10_1101-2020_10_26_351783 437 15 of of IN 10_1101-2020_10_26_351783 437 16 p38 p38 NN 10_1101-2020_10_26_351783 437 17 Mitogen- Mitogen- NNP 10_1101-2020_10_26_351783 437 18 Activated Activated NNP 10_1101-2020_10_26_351783 437 19 Protein Protein NNP 10_1101-2020_10_26_351783 437 20 Kinase Kinase NNP 10_1101-2020_10_26_351783 437 21 in in IN 10_1101-2020_10_26_351783 437 22 Multiple Multiple NNP 10_1101-2020_10_26_351783 437 23 Sclerosis Sclerosis NNP 10_1101-2020_10_26_351783 437 24 and and CC 10_1101-2020_10_26_351783 437 25 Its -PRON- PRP$ 10_1101-2020_10_26_351783 437 26 Models model NNS 10_1101-2020_10_26_351783 437 27 . . . 10_1101-2020_10_26_351783 438 1 Mol Mol NNP 10_1101-2020_10_26_351783 438 2 Cell Cell NNP 10_1101-2020_10_26_351783 438 3 Biol Biol NNP 10_1101-2020_10_26_351783 438 4 . . . 10_1101-2020_10_26_351783 439 1 2013;33:3728–34 2013;33:3728–34 CD 10_1101-2020_10_26_351783 439 2 . . . 10_1101-2020_10_26_351783 440 1 32 32 CD 10_1101-2020_10_26_351783 440 2 . . . 10_1101-2020_10_26_351783 441 1 Kotelnikova Kotelnikova NNP 10_1101-2020_10_26_351783 441 2 E E NNP 10_1101-2020_10_26_351783 441 3 , , , 10_1101-2020_10_26_351783 441 4 Kiani Kiani NNP 10_1101-2020_10_26_351783 441 5 NA NA NNP 10_1101-2020_10_26_351783 441 6 , , , 10_1101-2020_10_26_351783 441 7 Messinis Messinis NNP 10_1101-2020_10_26_351783 441 8 D D NNP 10_1101-2020_10_26_351783 441 9 , , , 10_1101-2020_10_26_351783 441 10 Pertsovskaya Pertsovskaya NNP 10_1101-2020_10_26_351783 441 11 I I NNP 10_1101-2020_10_26_351783 441 12 , , , 10_1101-2020_10_26_351783 441 13 Pliaka Pliaka NNP 10_1101-2020_10_26_351783 441 14 V V NNP 10_1101-2020_10_26_351783 441 15 , , , 10_1101-2020_10_26_351783 441 16 Bernardo Bernardo NNP 10_1101-2020_10_26_351783 441 17 - - HYPH 10_1101-2020_10_26_351783 441 18 Faura Faura NNP 10_1101-2020_10_26_351783 441 19 M M NNP 10_1101-2020_10_26_351783 441 20 , , , 10_1101-2020_10_26_351783 441 21 et et NNP 10_1101-2020_10_26_351783 441 22 al al NNP 10_1101-2020_10_26_351783 441 23 . . . 10_1101-2020_10_26_351783 442 1 MAPK MAPK NNP 10_1101-2020_10_26_351783 442 2 pathway pathway NN 10_1101-2020_10_26_351783 442 3 and and CC 10_1101-2020_10_26_351783 442 4 B b NN 10_1101-2020_10_26_351783 442 5 cells cell NNS 10_1101-2020_10_26_351783 442 6 overactivation overactivation NN 10_1101-2020_10_26_351783 442 7 in in IN 10_1101-2020_10_26_351783 442 8 multiple multiple JJ 10_1101-2020_10_26_351783 442 9 sclerosis sclerosis NN 10_1101-2020_10_26_351783 442 10 revealed reveal VBN 10_1101-2020_10_26_351783 442 11 by by IN 10_1101-2020_10_26_351783 442 12 phosphoproteomics phosphoproteomic NNS 10_1101-2020_10_26_351783 442 13 and and CC 10_1101-2020_10_26_351783 442 14 genomic genomic JJ 10_1101-2020_10_26_351783 442 15 analysis analysis NN 10_1101-2020_10_26_351783 442 16 . . . 10_1101-2020_10_26_351783 443 1 Proc Proc NNP 10_1101-2020_10_26_351783 443 2 Natl Natl NNP 10_1101-2020_10_26_351783 443 3 Acad Acad NNP 10_1101-2020_10_26_351783 443 4 Sci Sci NNP 10_1101-2020_10_26_351783 443 5 U U NNP 10_1101-2020_10_26_351783 443 6 S S NNP 10_1101-2020_10_26_351783 443 7 A. a. NN 10_1101-2020_10_26_351783 444 1 2019;116:9671–6 2019;116:9671–6 CD 10_1101-2020_10_26_351783 444 2 . . . 10_1101-2020_10_26_351783 445 1 33 33 CD 10_1101-2020_10_26_351783 445 2 . . . 10_1101-2020_10_26_351783 446 1 Kunkl Kunkl NNP 10_1101-2020_10_26_351783 446 2 M M NNP 10_1101-2020_10_26_351783 446 3 , , , 10_1101-2020_10_26_351783 446 4 Frascolla Frascolla NNP 10_1101-2020_10_26_351783 446 5 S S NNP 10_1101-2020_10_26_351783 446 6 , , , 10_1101-2020_10_26_351783 446 7 Amormino Amormino NNP 10_1101-2020_10_26_351783 446 8 C C NNP 10_1101-2020_10_26_351783 446 9 , , , 10_1101-2020_10_26_351783 446 10 Volpe Volpe NNP 10_1101-2020_10_26_351783 446 11 E E NNP 10_1101-2020_10_26_351783 446 12 , , , 10_1101-2020_10_26_351783 446 13 Tuosto Tuosto NNP 10_1101-2020_10_26_351783 446 14 L. L. NNP 10_1101-2020_10_26_351783 446 15 T T NNP 10_1101-2020_10_26_351783 446 16 Helper helper NN 10_1101-2020_10_26_351783 446 17 Cells Cells NNPS 10_1101-2020_10_26_351783 446 18 : : : 10_1101-2020_10_26_351783 446 19 The the DT 10_1101-2020_10_26_351783 446 20 Modulators modulator NNS 10_1101-2020_10_26_351783 446 21 of of IN 10_1101-2020_10_26_351783 446 22 Inflammation inflammation NN 10_1101-2020_10_26_351783 446 23 in in IN 10_1101-2020_10_26_351783 446 24 Multiple Multiple NNP 10_1101-2020_10_26_351783 446 25 Sclerosis Sclerosis NNP 10_1101-2020_10_26_351783 446 26 . . . 10_1101-2020_10_26_351783 447 1 Cells cell NNS 10_1101-2020_10_26_351783 447 2 . . . 10_1101-2020_10_26_351783 448 1 2020;9:482 2020;9:482 CD 10_1101-2020_10_26_351783 448 2 . . . 10_1101-2020_10_26_351783 449 1 34 34 CD 10_1101-2020_10_26_351783 449 2 . . . 10_1101-2020_10_26_351783 450 1 Waubant waubant NN 10_1101-2020_10_26_351783 450 2 E E NNP 10_1101-2020_10_26_351783 450 3 , , , 10_1101-2020_10_26_351783 450 4 Lucas Lucas NNP 10_1101-2020_10_26_351783 450 5 R R NNP 10_1101-2020_10_26_351783 450 6 , , , 10_1101-2020_10_26_351783 450 7 Mowry Mowry NNP 10_1101-2020_10_26_351783 450 8 E E NNP 10_1101-2020_10_26_351783 450 9 , , , 10_1101-2020_10_26_351783 450 10 Graves Graves NNP 10_1101-2020_10_26_351783 450 11 J J NNP 10_1101-2020_10_26_351783 450 12 , , , 10_1101-2020_10_26_351783 450 13 Olsson Olsson NNP 10_1101-2020_10_26_351783 450 14 T T NNP 10_1101-2020_10_26_351783 450 15 , , , 10_1101-2020_10_26_351783 450 16 Alfredsson Alfredsson NNP 10_1101-2020_10_26_351783 450 17 L L NNP 10_1101-2020_10_26_351783 450 18 , , , 10_1101-2020_10_26_351783 450 19 et et NNP 10_1101-2020_10_26_351783 450 20 al al NNP 10_1101-2020_10_26_351783 450 21 . . . 10_1101-2020_10_26_351783 451 1 Environmental environmental JJ 10_1101-2020_10_26_351783 451 2 and and CC 10_1101-2020_10_26_351783 451 3 genetic genetic JJ 10_1101-2020_10_26_351783 451 4 risk risk NN 10_1101-2020_10_26_351783 451 5 factors factor NNS 10_1101-2020_10_26_351783 451 6 for for IN 10_1101-2020_10_26_351783 451 7 MS MS NNP 10_1101-2020_10_26_351783 451 8 : : : 10_1101-2020_10_26_351783 451 9 an an DT 10_1101-2020_10_26_351783 451 10 integrated integrated JJ 10_1101-2020_10_26_351783 451 11 review review NN 10_1101-2020_10_26_351783 451 12 . . . 10_1101-2020_10_26_351783 452 1 Ann Ann NNP 10_1101-2020_10_26_351783 452 2 Clin Clin NNP 10_1101-2020_10_26_351783 452 3 Transl Transl NNP 10_1101-2020_10_26_351783 452 4 Neurol Neurol NNP 10_1101-2020_10_26_351783 452 5 . . . 10_1101-2020_10_26_351783 453 1 2019;6:1905–22 2019;6:1905–22 LS 10_1101-2020_10_26_351783 453 2 . . . 10_1101-2020_10_26_351783 454 1 35 35 CD 10_1101-2020_10_26_351783 454 2 . . . 10_1101-2020_10_26_351783 455 1 Olsson Olsson NNP 10_1101-2020_10_26_351783 455 2 T T NNP 10_1101-2020_10_26_351783 455 3 , , , 10_1101-2020_10_26_351783 455 4 Barcellos Barcellos NNP 10_1101-2020_10_26_351783 455 5 LF LF NNP 10_1101-2020_10_26_351783 455 6 , , , 10_1101-2020_10_26_351783 455 7 Alfredsson Alfredsson NNP 10_1101-2020_10_26_351783 455 8 L. L. NNP 10_1101-2020_10_26_351783 455 9 Interactions Interactions NNP 10_1101-2020_10_26_351783 455 10 between between IN 10_1101-2020_10_26_351783 455 11 genetic genetic JJ 10_1101-2020_10_26_351783 455 12 , , , 10_1101-2020_10_26_351783 455 13 lifestyle lifestyle NN 10_1101-2020_10_26_351783 455 14 and and CC 10_1101-2020_10_26_351783 455 15 environmental environmental JJ 10_1101-2020_10_26_351783 455 16 risk risk NN 10_1101-2020_10_26_351783 455 17 factors factor NNS 10_1101-2020_10_26_351783 455 18 for for IN 10_1101-2020_10_26_351783 455 19 multiple multiple JJ 10_1101-2020_10_26_351783 455 20 sclerosis sclerosis NN 10_1101-2020_10_26_351783 455 21 . . . 10_1101-2020_10_26_351783 456 1 Nat Nat NNP 10_1101-2020_10_26_351783 456 2 Rev Rev NNP 10_1101-2020_10_26_351783 456 3 Neurol Neurol NNP 10_1101-2020_10_26_351783 456 4 . . . 10_1101-2020_10_26_351783 457 1 Nature Nature NNP 10_1101-2020_10_26_351783 457 2 Publishing Publishing NNP 10_1101-2020_10_26_351783 457 3 Group Group NNP 10_1101-2020_10_26_351783 457 4 ; ; : 10_1101-2020_10_26_351783 457 5 2016;13:26–36 2016;13:26–36 CD 10_1101-2020_10_26_351783 457 6 . . . 10_1101-2020_10_26_351783 458 1 36 36 CD 10_1101-2020_10_26_351783 458 2 . . . 10_1101-2020_10_26_351783 459 1 Kular Kular NNP 10_1101-2020_10_26_351783 459 2 L L NNP 10_1101-2020_10_26_351783 459 3 , , , 10_1101-2020_10_26_351783 459 4 Liu Liu NNP 10_1101-2020_10_26_351783 459 5 Y Y NNP 10_1101-2020_10_26_351783 459 6 , , , 10_1101-2020_10_26_351783 459 7 Ruhrmann Ruhrmann NNP 10_1101-2020_10_26_351783 459 8 S S NNP 10_1101-2020_10_26_351783 459 9 , , , 10_1101-2020_10_26_351783 459 10 Zheleznyakova Zheleznyakova NNP 10_1101-2020_10_26_351783 459 11 G G NNP 10_1101-2020_10_26_351783 459 12 , , , 10_1101-2020_10_26_351783 459 13 Marabita Marabita NNP 10_1101-2020_10_26_351783 459 14 F F NNP 10_1101-2020_10_26_351783 459 15 , , , 10_1101-2020_10_26_351783 459 16 Gomez Gomez NNP 10_1101-2020_10_26_351783 459 17 - - HYPH 10_1101-2020_10_26_351783 459 18 Cabrero Cabrero NNP 10_1101-2020_10_26_351783 459 19 D D NNP 10_1101-2020_10_26_351783 459 20 , , , 10_1101-2020_10_26_351783 459 21 et et NNP 10_1101-2020_10_26_351783 459 22 al al NNP 10_1101-2020_10_26_351783 459 23 . . . 10_1101-2020_10_26_351783 460 1 DNA dna NN 10_1101-2020_10_26_351783 460 2 methylation methylation NN 10_1101-2020_10_26_351783 460 3 as as IN 10_1101-2020_10_26_351783 460 4 a a DT 10_1101-2020_10_26_351783 460 5 mediator mediator NN 10_1101-2020_10_26_351783 460 6 of of IN 10_1101-2020_10_26_351783 460 7 HLA HLA NNP 10_1101-2020_10_26_351783 460 8 - - HYPH 10_1101-2020_10_26_351783 460 9 DRB1 DRB1 NNP 10_1101-2020_10_26_351783 460 10 15:01 15:01 CD 10_1101-2020_10_26_351783 460 11 and and CC 10_1101-2020_10_26_351783 460 12 a a DT 10_1101-2020_10_26_351783 460 13 protective protective JJ 10_1101-2020_10_26_351783 460 14 variant variant NN 10_1101-2020_10_26_351783 460 15 in in IN 10_1101-2020_10_26_351783 460 16 multiple multiple JJ 10_1101-2020_10_26_351783 460 17 sclerosis sclerosis NN 10_1101-2020_10_26_351783 460 18 . . . 10_1101-2020_10_26_351783 461 1 Nat Nat NNP 10_1101-2020_10_26_351783 461 2 ( ( -LRB- 10_1101-2020_10_26_351783 461 3 which which WDT 10_1101-2020_10_26_351783 461 4 was be VBD 10_1101-2020_10_26_351783 461 5 not not RB 10_1101-2020_10_26_351783 461 6 certified certify VBN 10_1101-2020_10_26_351783 461 7 by by IN 10_1101-2020_10_26_351783 461 8 peer peer NN 10_1101-2020_10_26_351783 461 9 review review NN 10_1101-2020_10_26_351783 461 10 ) ) -RRB- 10_1101-2020_10_26_351783 461 11 is be VBZ 10_1101-2020_10_26_351783 461 12 the the DT 10_1101-2020_10_26_351783 461 13 author author NN 10_1101-2020_10_26_351783 461 14 / / SYM 10_1101-2020_10_26_351783 461 15 funder funder NN 10_1101-2020_10_26_351783 461 16 . . . 10_1101-2020_10_26_351783 462 1 All all DT 10_1101-2020_10_26_351783 462 2 rights right NNS 10_1101-2020_10_26_351783 462 3 reserved reserve VBD 10_1101-2020_10_26_351783 462 4 . . . 10_1101-2020_10_26_351783 463 1 No no DT 10_1101-2020_10_26_351783 463 2 reuse reuse NN 10_1101-2020_10_26_351783 463 3 allowed allow VBN 10_1101-2020_10_26_351783 463 4 without without IN 10_1101-2020_10_26_351783 463 5 permission permission NN 10_1101-2020_10_26_351783 463 6 . . . 10_1101-2020_10_26_351783 464 1 The the DT 10_1101-2020_10_26_351783 464 2 copyright copyright NN 10_1101-2020_10_26_351783 464 3 holder holder NN 10_1101-2020_10_26_351783 464 4 for for IN 10_1101-2020_10_26_351783 464 5 this this DT 10_1101-2020_10_26_351783 464 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 464 7 version version NN 10_1101-2020_10_26_351783 464 8 posted post VBD 10_1101-2020_10_26_351783 464 9 January January NNP 10_1101-2020_10_26_351783 464 10 6 6 CD 10_1101-2020_10_26_351783 464 11 , , , 10_1101-2020_10_26_351783 464 12 2021 2021 CD 10_1101-2020_10_26_351783 464 13 . . . 10_1101-2020_10_26_351783 464 14 ; ; : 10_1101-2020_10_26_351783 464 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 464 16 : : : 10_1101-2020_10_26_351783 464 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 464 18 preprint preprint NN 10_1101-2020_10_26_351783 464 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 464 20 24 24 CD 10_1101-2020_10_26_351783 464 21 Commun commun NN 10_1101-2020_10_26_351783 464 22 . . . 10_1101-2020_10_26_351783 465 1 2018;9 2018;9 LS 10_1101-2020_10_26_351783 465 2 . . . 10_1101-2020_10_26_351783 466 1 37 37 CD 10_1101-2020_10_26_351783 466 2 . . . 10_1101-2020_10_26_351783 467 1 Compston Compston NNP 10_1101-2020_10_26_351783 467 2 A A NNP 10_1101-2020_10_26_351783 467 3 , , , 10_1101-2020_10_26_351783 467 4 Coles Coles NNP 10_1101-2020_10_26_351783 467 5 A. a. NN 10_1101-2020_10_26_351783 468 1 Multiple multiple JJ 10_1101-2020_10_26_351783 468 2 sclerosis sclerosis NN 10_1101-2020_10_26_351783 468 3 . . . 10_1101-2020_10_26_351783 469 1 Lancet Lancet NNP 10_1101-2020_10_26_351783 469 2 [ [ -LRB- 10_1101-2020_10_26_351783 469 3 Internet internet NN 10_1101-2020_10_26_351783 469 4 ] ] -RRB- 10_1101-2020_10_26_351783 469 5 . . . 10_1101-2020_10_26_351783 470 1 Elsevier Elsevier NNP 10_1101-2020_10_26_351783 470 2 Ltd Ltd NNP 10_1101-2020_10_26_351783 470 3 ; ; : 10_1101-2020_10_26_351783 470 4 2008;372:1502–17 2008;372:1502–17 CD 10_1101-2020_10_26_351783 470 5 . . . 10_1101-2020_10_26_351783 471 1 Available available JJ 10_1101-2020_10_26_351783 471 2 from from IN 10_1101-2020_10_26_351783 471 3 : : : 10_1101-2020_10_26_351783 471 4 http://dx.doi.org/10.1016/S0140-6736(08)61620-7 http://dx.doi.org/10.1016/S0140-6736(08)61620-7 NNP 10_1101-2020_10_26_351783 471 5 38 38 CD 10_1101-2020_10_26_351783 471 6 . . . 10_1101-2020_10_26_351783 472 1 Jelcic Jelcic NNP 10_1101-2020_10_26_351783 472 2 I -PRON- PRP 10_1101-2020_10_26_351783 472 3 , , , 10_1101-2020_10_26_351783 472 4 Al Al NNP 10_1101-2020_10_26_351783 472 5 Nimer Nimer NNP 10_1101-2020_10_26_351783 472 6 F F NNP 10_1101-2020_10_26_351783 472 7 , , , 10_1101-2020_10_26_351783 472 8 Wang Wang NNP 10_1101-2020_10_26_351783 472 9 J J NNP 10_1101-2020_10_26_351783 472 10 , , , 10_1101-2020_10_26_351783 472 11 Lentsch Lentsch NNP 10_1101-2020_10_26_351783 472 12 V V NNP 10_1101-2020_10_26_351783 472 13 , , , 10_1101-2020_10_26_351783 472 14 Planas Planas NNP 10_1101-2020_10_26_351783 472 15 R R NNP 10_1101-2020_10_26_351783 472 16 , , , 10_1101-2020_10_26_351783 472 17 Jelcic Jelcic NNP 10_1101-2020_10_26_351783 472 18 I I NNP 10_1101-2020_10_26_351783 472 19 , , , 10_1101-2020_10_26_351783 472 20 et et NNP 10_1101-2020_10_26_351783 472 21 al al NNP 10_1101-2020_10_26_351783 472 22 . . . 10_1101-2020_10_26_351783 473 1 Memory memory NN 10_1101-2020_10_26_351783 473 2 B B NNP 10_1101-2020_10_26_351783 473 3 Cells cell NNS 10_1101-2020_10_26_351783 473 4 Activate activate VBP 10_1101-2020_10_26_351783 473 5 Brain- Brain- NNP 10_1101-2020_10_26_351783 473 6 Homing Homing NNP 10_1101-2020_10_26_351783 473 7 , , , 10_1101-2020_10_26_351783 473 8 Autoreactive Autoreactive NNP 10_1101-2020_10_26_351783 473 9 CD4 cd4 NN 10_1101-2020_10_26_351783 473 10 + + SYM 10_1101-2020_10_26_351783 473 11 T t NN 10_1101-2020_10_26_351783 473 12 Cells cell NNS 10_1101-2020_10_26_351783 473 13 in in IN 10_1101-2020_10_26_351783 473 14 Multiple Multiple NNP 10_1101-2020_10_26_351783 473 15 Sclerosis Sclerosis NNP 10_1101-2020_10_26_351783 473 16 . . . 10_1101-2020_10_26_351783 474 1 Cell cell NN 10_1101-2020_10_26_351783 474 2 . . . 10_1101-2020_10_26_351783 475 1 2018;175:85 2018;175:85 LS 10_1101-2020_10_26_351783 475 2 - - SYM 10_1101-2020_10_26_351783 475 3 100.e23 100.e23 NNP 10_1101-2020_10_26_351783 475 4 . . . 10_1101-2020_10_26_351783 476 1 39 39 CD 10_1101-2020_10_26_351783 476 2 . . . 10_1101-2020_10_26_351783 477 1 Lange Lange NNP 10_1101-2020_10_26_351783 477 2 C C NNP 10_1101-2020_10_26_351783 477 3 , , , 10_1101-2020_10_26_351783 477 4 Storkebaum Storkebaum NNP 10_1101-2020_10_26_351783 477 5 E E NNP 10_1101-2020_10_26_351783 477 6 , , , 10_1101-2020_10_26_351783 477 7 De De NNP 10_1101-2020_10_26_351783 477 8 Almodóvar Almodóvar NNP 10_1101-2020_10_26_351783 477 9 CR CR NNP 10_1101-2020_10_26_351783 477 10 , , , 10_1101-2020_10_26_351783 477 11 Dewerchin Dewerchin NNP 10_1101-2020_10_26_351783 477 12 M M NNP 10_1101-2020_10_26_351783 477 13 , , , 10_1101-2020_10_26_351783 477 14 Carmeliet Carmeliet NNP 10_1101-2020_10_26_351783 477 15 P. P. NNP 10_1101-2020_10_26_351783 477 16 Vascular vascular JJ 10_1101-2020_10_26_351783 477 17 endothelial endothelial JJ 10_1101-2020_10_26_351783 477 18 growth growth NN 10_1101-2020_10_26_351783 477 19 factor factor NN 10_1101-2020_10_26_351783 477 20 : : : 10_1101-2020_10_26_351783 477 21 A a DT 10_1101-2020_10_26_351783 477 22 neurovascular neurovascular JJ 10_1101-2020_10_26_351783 477 23 target target NN 10_1101-2020_10_26_351783 477 24 in in IN 10_1101-2020_10_26_351783 477 25 neurological neurological JJ 10_1101-2020_10_26_351783 477 26 diseases disease NNS 10_1101-2020_10_26_351783 477 27 . . . 10_1101-2020_10_26_351783 478 1 Nat Nat NNP 10_1101-2020_10_26_351783 478 2 Rev Rev NNP 10_1101-2020_10_26_351783 478 3 Neurol Neurol NNP 10_1101-2020_10_26_351783 478 4 [ [ -LRB- 10_1101-2020_10_26_351783 478 5 Internet internet NN 10_1101-2020_10_26_351783 478 6 ] ] -RRB- 10_1101-2020_10_26_351783 478 7 . . . 10_1101-2020_10_26_351783 479 1 Nature Nature NNP 10_1101-2020_10_26_351783 479 2 Publishing Publishing NNP 10_1101-2020_10_26_351783 479 3 Group Group NNP 10_1101-2020_10_26_351783 479 4 ; ; : 10_1101-2020_10_26_351783 479 5 2016;12:439–54 2016;12:439–54 NNP 10_1101-2020_10_26_351783 479 6 . . . 10_1101-2020_10_26_351783 480 1 Available available JJ 10_1101-2020_10_26_351783 480 2 from from IN 10_1101-2020_10_26_351783 480 3 : : : 10_1101-2020_10_26_351783 480 4 http://dx.doi.org/10.1038/nrneurol.2016.88 http://dx.doi.org/10.1038/nrneurol.2016.88 NNP 10_1101-2020_10_26_351783 480 5 ( ( -LRB- 10_1101-2020_10_26_351783 480 6 which which WDT 10_1101-2020_10_26_351783 480 7 was be VBD 10_1101-2020_10_26_351783 480 8 not not RB 10_1101-2020_10_26_351783 480 9 certified certify VBN 10_1101-2020_10_26_351783 480 10 by by IN 10_1101-2020_10_26_351783 480 11 peer peer NN 10_1101-2020_10_26_351783 480 12 review review NN 10_1101-2020_10_26_351783 480 13 ) ) -RRB- 10_1101-2020_10_26_351783 480 14 is be VBZ 10_1101-2020_10_26_351783 480 15 the the DT 10_1101-2020_10_26_351783 480 16 author author NN 10_1101-2020_10_26_351783 480 17 / / SYM 10_1101-2020_10_26_351783 480 18 funder funder NN 10_1101-2020_10_26_351783 480 19 . . . 10_1101-2020_10_26_351783 481 1 All all DT 10_1101-2020_10_26_351783 481 2 rights right NNS 10_1101-2020_10_26_351783 481 3 reserved reserve VBD 10_1101-2020_10_26_351783 481 4 . . . 10_1101-2020_10_26_351783 482 1 No no DT 10_1101-2020_10_26_351783 482 2 reuse reuse NN 10_1101-2020_10_26_351783 482 3 allowed allow VBN 10_1101-2020_10_26_351783 482 4 without without IN 10_1101-2020_10_26_351783 482 5 permission permission NN 10_1101-2020_10_26_351783 482 6 . . . 10_1101-2020_10_26_351783 483 1 The the DT 10_1101-2020_10_26_351783 483 2 copyright copyright NN 10_1101-2020_10_26_351783 483 3 holder holder NN 10_1101-2020_10_26_351783 483 4 for for IN 10_1101-2020_10_26_351783 483 5 this this DT 10_1101-2020_10_26_351783 483 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 483 7 version version NN 10_1101-2020_10_26_351783 483 8 posted post VBD 10_1101-2020_10_26_351783 483 9 January January NNP 10_1101-2020_10_26_351783 483 10 6 6 CD 10_1101-2020_10_26_351783 483 11 , , , 10_1101-2020_10_26_351783 483 12 2021 2021 CD 10_1101-2020_10_26_351783 483 13 . . . 10_1101-2020_10_26_351783 483 14 ; ; : 10_1101-2020_10_26_351783 483 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 483 16 : : : 10_1101-2020_10_26_351783 483 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 483 18 preprint preprint NN 10_1101-2020_10_26_351783 483 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CD 10_1101-2020_10_26_351783 483 20 Figures figure NNS 10_1101-2020_10_26_351783 483 21 : : : 10_1101-2020_10_26_351783 483 22 Figure figure NN 10_1101-2020_10_26_351783 483 23 1 1 CD 10_1101-2020_10_26_351783 483 24 . . . 10_1101-2020_10_26_351783 484 1 Overview overview NN 10_1101-2020_10_26_351783 484 2 of of IN 10_1101-2020_10_26_351783 484 3 the the DT 10_1101-2020_10_26_351783 484 4 benchmark benchmark NN 10_1101-2020_10_26_351783 484 5 assessment assessment NN 10_1101-2020_10_26_351783 484 6 of of IN 10_1101-2020_10_26_351783 484 7 disease disease NNP 10_1101-2020_10_26_351783 484 8 modules module NNS 10_1101-2020_10_26_351783 484 9 and and CC 10_1101-2020_10_26_351783 484 10 the the DT 10_1101-2020_10_26_351783 484 11 integration integration NN 10_1101-2020_10_26_351783 484 12 workflow workflow NN 10_1101-2020_10_26_351783 484 13 for for IN 10_1101-2020_10_26_351783 484 14 MS MS NNP 10_1101-2020_10_26_351783 484 15 . . . 10_1101-2020_10_26_351783 484 16 ( ( -LRB- 10_1101-2020_10_26_351783 484 17 a a LS 10_1101-2020_10_26_351783 484 18 ) ) -RRB- 10_1101-2020_10_26_351783 484 19 Transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 484 20 and and CC 10_1101-2020_10_26_351783 484 21 methylomic methylomic JJ 10_1101-2020_10_26_351783 484 22 datasets dataset NNS 10_1101-2020_10_26_351783 484 23 from from IN 10_1101-2020_10_26_351783 484 24 19 19 CD 10_1101-2020_10_26_351783 484 25 different different JJ 10_1101-2020_10_26_351783 484 26 diseases disease NNS 10_1101-2020_10_26_351783 484 27 were be VBD 10_1101-2020_10_26_351783 484 28 used use VBN 10_1101-2020_10_26_351783 484 29 as as IN 10_1101-2020_10_26_351783 484 30 inputs input NNS 10_1101-2020_10_26_351783 484 31 for for IN 10_1101-2020_10_26_351783 484 32 eight eight CD 10_1101-2020_10_26_351783 484 33 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 484 34 module module JJ 10_1101-2020_10_26_351783 484 35 identification identification NN 10_1101-2020_10_26_351783 484 36 methods method NNS 10_1101-2020_10_26_351783 484 37 . . . 10_1101-2020_10_26_351783 485 1 The the DT 10_1101-2020_10_26_351783 485 2 resulting result VBG 10_1101-2020_10_26_351783 485 3 single single JJ 10_1101-2020_10_26_351783 485 4 - - HYPH 10_1101-2020_10_26_351783 485 5 omic omic JJ 10_1101-2020_10_26_351783 485 6 disease disease NN 10_1101-2020_10_26_351783 485 7 modules module NNS 10_1101-2020_10_26_351783 485 8 ( ( -LRB- 10_1101-2020_10_26_351783 485 9 n n NNP 10_1101-2020_10_26_351783 485 10 = = SYM 10_1101-2020_10_26_351783 485 11 ( ( -LRB- 10_1101-2020_10_26_351783 485 12 which which WDT 10_1101-2020_10_26_351783 485 13 was be VBD 10_1101-2020_10_26_351783 485 14 not not RB 10_1101-2020_10_26_351783 485 15 certified certify VBN 10_1101-2020_10_26_351783 485 16 by by IN 10_1101-2020_10_26_351783 485 17 peer peer NN 10_1101-2020_10_26_351783 485 18 review review NN 10_1101-2020_10_26_351783 485 19 ) ) -RRB- 10_1101-2020_10_26_351783 485 20 is be VBZ 10_1101-2020_10_26_351783 485 21 the the DT 10_1101-2020_10_26_351783 485 22 author author NN 10_1101-2020_10_26_351783 485 23 / / SYM 10_1101-2020_10_26_351783 485 24 funder funder NN 10_1101-2020_10_26_351783 485 25 . . . 10_1101-2020_10_26_351783 486 1 All all DT 10_1101-2020_10_26_351783 486 2 rights right NNS 10_1101-2020_10_26_351783 486 3 reserved reserve VBD 10_1101-2020_10_26_351783 486 4 . . . 10_1101-2020_10_26_351783 487 1 No no DT 10_1101-2020_10_26_351783 487 2 reuse reuse NN 10_1101-2020_10_26_351783 487 3 allowed allow VBN 10_1101-2020_10_26_351783 487 4 without without IN 10_1101-2020_10_26_351783 487 5 permission permission NN 10_1101-2020_10_26_351783 487 6 . . . 10_1101-2020_10_26_351783 488 1 The the DT 10_1101-2020_10_26_351783 488 2 copyright copyright NN 10_1101-2020_10_26_351783 488 3 holder holder NN 10_1101-2020_10_26_351783 488 4 for for IN 10_1101-2020_10_26_351783 488 5 this this DT 10_1101-2020_10_26_351783 488 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 488 7 version version NN 10_1101-2020_10_26_351783 488 8 posted post VBD 10_1101-2020_10_26_351783 488 9 January January NNP 10_1101-2020_10_26_351783 488 10 6 6 CD 10_1101-2020_10_26_351783 488 11 , , , 10_1101-2020_10_26_351783 488 12 2021 2021 CD 10_1101-2020_10_26_351783 488 13 . . . 10_1101-2020_10_26_351783 488 14 ; ; : 10_1101-2020_10_26_351783 488 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 488 16 : : : 10_1101-2020_10_26_351783 488 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 488 18 preprint preprint NN 10_1101-2020_10_26_351783 488 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 488 20 26 26 CD 10_1101-2020_10_26_351783 488 21 456 456 CD 10_1101-2020_10_26_351783 488 22 ) ) -RRB- 10_1101-2020_10_26_351783 488 23 were be VBD 10_1101-2020_10_26_351783 488 24 independently independently RB 10_1101-2020_10_26_351783 488 25 assessed assess VBN 10_1101-2020_10_26_351783 488 26 by by IN 10_1101-2020_10_26_351783 488 27 GWAS GWAS NNP 10_1101-2020_10_26_351783 488 28 enrichment enrichment NN 10_1101-2020_10_26_351783 488 29 analysis analysis NN 10_1101-2020_10_26_351783 488 30 of of IN 10_1101-2020_10_26_351783 488 31 the the DT 10_1101-2020_10_26_351783 488 32 same same JJ 10_1101-2020_10_26_351783 488 33 disease disease NN 10_1101-2020_10_26_351783 488 34 using use VBG 10_1101-2020_10_26_351783 488 35 Pascal pascal JJ 10_1101-2020_10_26_351783 488 36 module module NN 10_1101-2020_10_26_351783 488 37 scoring score VBG 10_1101-2020_10_26_351783 488 38 . . . 10_1101-2020_10_26_351783 489 1 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 489 2 methods method NNS 10_1101-2020_10_26_351783 489 3 were be VBD 10_1101-2020_10_26_351783 489 4 evaluated evaluate VBN 10_1101-2020_10_26_351783 489 5 by by IN 10_1101-2020_10_26_351783 489 6 the the DT 10_1101-2020_10_26_351783 489 7 combined combine VBN 10_1101-2020_10_26_351783 489 8 enrichment enrichment NN 10_1101-2020_10_26_351783 489 9 score score NN 10_1101-2020_10_26_351783 489 10 of of IN 10_1101-2020_10_26_351783 489 11 their -PRON- PRP$ 10_1101-2020_10_26_351783 489 12 respective respective JJ 10_1101-2020_10_26_351783 489 13 disease disease NN 10_1101-2020_10_26_351783 489 14 modules module NNS 10_1101-2020_10_26_351783 489 15 . . . 10_1101-2020_10_26_351783 490 1 ( ( -LRB- 10_1101-2020_10_26_351783 490 2 b b LS 10_1101-2020_10_26_351783 490 3 ) ) -RRB- 10_1101-2020_10_26_351783 490 4 Multi multi JJ 10_1101-2020_10_26_351783 490 5 - - JJ 10_1101-2020_10_26_351783 490 6 omic omic JJ 10_1101-2020_10_26_351783 490 7 integrative integrative JJ 10_1101-2020_10_26_351783 490 8 workflow workflow NN 10_1101-2020_10_26_351783 490 9 for for IN 10_1101-2020_10_26_351783 490 10 multiple multiple JJ 10_1101-2020_10_26_351783 490 11 sclerosis sclerosis NN 10_1101-2020_10_26_351783 490 12 ( ( -LRB- 10_1101-2020_10_26_351783 490 13 MS)- MS)- NNP 10_1101-2020_10_26_351783 490 14 associated associate VBN 10_1101-2020_10_26_351783 490 15 modules module NNS 10_1101-2020_10_26_351783 490 16 . . . 10_1101-2020_10_26_351783 491 1 Data datum NNS 10_1101-2020_10_26_351783 491 2 from from IN 10_1101-2020_10_26_351783 491 3 20 20 CD 10_1101-2020_10_26_351783 491 4 case case NN 10_1101-2020_10_26_351783 491 5 - - HYPH 10_1101-2020_10_26_351783 491 6 control control NN 10_1101-2020_10_26_351783 491 7 comparisons comparison NNS 10_1101-2020_10_26_351783 491 8 were be VBD 10_1101-2020_10_26_351783 491 9 used use VBN 10_1101-2020_10_26_351783 491 10 as as IN 10_1101-2020_10_26_351783 491 11 input input NN 10_1101-2020_10_26_351783 491 12 for for IN 10_1101-2020_10_26_351783 491 13 module module JJ 10_1101-2020_10_26_351783 491 14 detection detection NN 10_1101-2020_10_26_351783 491 15 with with IN 10_1101-2020_10_26_351783 491 16 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 491 17 methods method NNS 10_1101-2020_10_26_351783 491 18 . . . 10_1101-2020_10_26_351783 492 1 Clique Clique NNP 10_1101-2020_10_26_351783 492 2 SuM SuM NNP 10_1101-2020_10_26_351783 492 3 modules module NNS 10_1101-2020_10_26_351783 492 4 presented present VBD 10_1101-2020_10_26_351783 492 5 the the DT 10_1101-2020_10_26_351783 492 6 highest high JJS 10_1101-2020_10_26_351783 492 7 GWAS GWAS NNP 10_1101-2020_10_26_351783 492 8 enrichment enrichment NN 10_1101-2020_10_26_351783 492 9 score score NN 10_1101-2020_10_26_351783 492 10 and and CC 10_1101-2020_10_26_351783 492 11 were be VBD 10_1101-2020_10_26_351783 492 12 therefore therefore RB 10_1101-2020_10_26_351783 492 13 used use VBN 10_1101-2020_10_26_351783 492 14 to to TO 10_1101-2020_10_26_351783 492 15 generate generate VB 10_1101-2020_10_26_351783 492 16 single single JJ 10_1101-2020_10_26_351783 492 17 - - HYPH 10_1101-2020_10_26_351783 492 18 omic omic JJ 10_1101-2020_10_26_351783 492 19 consensus consensus NN 10_1101-2020_10_26_351783 492 20 modules module NNS 10_1101-2020_10_26_351783 492 21 . . . 10_1101-2020_10_26_351783 493 1 The the DT 10_1101-2020_10_26_351783 493 2 intersection intersection NN 10_1101-2020_10_26_351783 493 3 of of IN 10_1101-2020_10_26_351783 493 4 the the DT 10_1101-2020_10_26_351783 493 5 best good JJS 10_1101-2020_10_26_351783 493 6 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 493 7 and and CC 10_1101-2020_10_26_351783 493 8 methylomic methylomic JJ 10_1101-2020_10_26_351783 493 9 consensus consensus NN 10_1101-2020_10_26_351783 493 10 modules module NNS 10_1101-2020_10_26_351783 493 11 resulted result VBD 10_1101-2020_10_26_351783 493 12 in in IN 10_1101-2020_10_26_351783 493 13 an an DT 10_1101-2020_10_26_351783 493 14 MS MS NNP 10_1101-2020_10_26_351783 493 15 multi multi JJ 10_1101-2020_10_26_351783 493 16 - - JJ 10_1101-2020_10_26_351783 493 17 omic omic JJ 10_1101-2020_10_26_351783 493 18 module module NN 10_1101-2020_10_26_351783 493 19 ( ( -LRB- 10_1101-2020_10_26_351783 493 20 n n NNP 10_1101-2020_10_26_351783 493 21 = = SYM 10_1101-2020_10_26_351783 493 22 220 220 CD 10_1101-2020_10_26_351783 493 23 genes gene NNS 10_1101-2020_10_26_351783 493 24 ) ) -RRB- 10_1101-2020_10_26_351783 493 25 with with IN 10_1101-2020_10_26_351783 493 26 the the DT 10_1101-2020_10_26_351783 493 27 highest high JJS 10_1101-2020_10_26_351783 493 28 GWAS GWAS NNP 10_1101-2020_10_26_351783 493 29 enrichment enrichment NN 10_1101-2020_10_26_351783 493 30 , , , 10_1101-2020_10_26_351783 493 31 which which WDT 10_1101-2020_10_26_351783 493 32 was be VBD 10_1101-2020_10_26_351783 493 33 independently independently RB 10_1101-2020_10_26_351783 493 34 found find VBN 10_1101-2020_10_26_351783 493 35 to to TO 10_1101-2020_10_26_351783 493 36 be be VB 10_1101-2020_10_26_351783 493 37 enriched enrich VBN 10_1101-2020_10_26_351783 493 38 for for IN 10_1101-2020_10_26_351783 493 39 genes gene NNS 10_1101-2020_10_26_351783 493 40 associated associate VBN 10_1101-2020_10_26_351783 493 41 with with IN 10_1101-2020_10_26_351783 493 42 five five CD 10_1101-2020_10_26_351783 493 43 known know VBN 10_1101-2020_10_26_351783 493 44 lifestyle lifestyle NN 10_1101-2020_10_26_351783 493 45 MS MS NNP 10_1101-2020_10_26_351783 493 46 risk risk NN 10_1101-2020_10_26_351783 493 47 factors factor NNS 10_1101-2020_10_26_351783 493 48 using use VBG 10_1101-2020_10_26_351783 493 49 public public JJ 10_1101-2020_10_26_351783 493 50 omics omic NNS 10_1101-2020_10_26_351783 493 51 data datum NNS 10_1101-2020_10_26_351783 493 52 from from IN 10_1101-2020_10_26_351783 493 53 healthy healthy JJ 10_1101-2020_10_26_351783 493 54 individuals individual NNS 10_1101-2020_10_26_351783 493 55 . . . 10_1101-2020_10_26_351783 494 1 ( ( -LRB- 10_1101-2020_10_26_351783 494 2 which which WDT 10_1101-2020_10_26_351783 494 3 was be VBD 10_1101-2020_10_26_351783 494 4 not not RB 10_1101-2020_10_26_351783 494 5 certified certify VBN 10_1101-2020_10_26_351783 494 6 by by IN 10_1101-2020_10_26_351783 494 7 peer peer NN 10_1101-2020_10_26_351783 494 8 review review NN 10_1101-2020_10_26_351783 494 9 ) ) -RRB- 10_1101-2020_10_26_351783 494 10 is be VBZ 10_1101-2020_10_26_351783 494 11 the the DT 10_1101-2020_10_26_351783 494 12 author author NN 10_1101-2020_10_26_351783 494 13 / / SYM 10_1101-2020_10_26_351783 494 14 funder funder NN 10_1101-2020_10_26_351783 494 15 . . . 10_1101-2020_10_26_351783 495 1 All all DT 10_1101-2020_10_26_351783 495 2 rights right NNS 10_1101-2020_10_26_351783 495 3 reserved reserve VBD 10_1101-2020_10_26_351783 495 4 . . . 10_1101-2020_10_26_351783 496 1 No no DT 10_1101-2020_10_26_351783 496 2 reuse reuse NN 10_1101-2020_10_26_351783 496 3 allowed allow VBN 10_1101-2020_10_26_351783 496 4 without without IN 10_1101-2020_10_26_351783 496 5 permission permission NN 10_1101-2020_10_26_351783 496 6 . . . 10_1101-2020_10_26_351783 497 1 The the DT 10_1101-2020_10_26_351783 497 2 copyright copyright NN 10_1101-2020_10_26_351783 497 3 holder holder NN 10_1101-2020_10_26_351783 497 4 for for IN 10_1101-2020_10_26_351783 497 5 this this DT 10_1101-2020_10_26_351783 497 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 497 7 version version NN 10_1101-2020_10_26_351783 497 8 posted post VBD 10_1101-2020_10_26_351783 497 9 January January NNP 10_1101-2020_10_26_351783 497 10 6 6 CD 10_1101-2020_10_26_351783 497 11 , , , 10_1101-2020_10_26_351783 497 12 2021 2021 CD 10_1101-2020_10_26_351783 497 13 . . . 10_1101-2020_10_26_351783 497 14 ; ; : 10_1101-2020_10_26_351783 497 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 497 16 : : : 10_1101-2020_10_26_351783 497 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 497 18 preprint preprint NN 10_1101-2020_10_26_351783 497 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 497 20 Figure figure NN 10_1101-2020_10_26_351783 497 21 2 2 CD 10_1101-2020_10_26_351783 497 22 . . . 10_1101-2020_10_26_351783 498 1 Genomic genomic JJ 10_1101-2020_10_26_351783 498 2 concordance concordance NN 10_1101-2020_10_26_351783 498 3 of of IN 10_1101-2020_10_26_351783 498 4 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 498 5 modules module NNS 10_1101-2020_10_26_351783 498 6 on on IN 10_1101-2020_10_26_351783 498 7 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 498 8 datasets dataset NNS 10_1101-2020_10_26_351783 498 9 . . . 10_1101-2020_10_26_351783 499 1 ( ( -LRB- 10_1101-2020_10_26_351783 499 2 a a DT 10_1101-2020_10_26_351783 499 3 ) ) -RRB- 10_1101-2020_10_26_351783 499 4 Heatmap Heatmap NNP 10_1101-2020_10_26_351783 499 5 of of IN 10_1101-2020_10_26_351783 499 6 PASCAL PASCAL NNP 10_1101-2020_10_26_351783 499 7 p p NN 10_1101-2020_10_26_351783 499 8 - - HYPH 10_1101-2020_10_26_351783 499 9 values value NNS 10_1101-2020_10_26_351783 499 10 for for IN 10_1101-2020_10_26_351783 499 11 eight eight CD 10_1101-2020_10_26_351783 499 12 single single JJ 10_1101-2020_10_26_351783 499 13 - - HYPH 10_1101-2020_10_26_351783 499 14 method method NN 10_1101-2020_10_26_351783 499 15 and and CC 10_1101-2020_10_26_351783 499 16 eight eight CD 10_1101-2020_10_26_351783 499 17 consensus consensus NN 10_1101-2020_10_26_351783 499 18 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 499 19 modules modules NNP 10_1101-2020_10_26_351783 499 20 , , , 10_1101-2020_10_26_351783 499 21 identified identify VBN 10_1101-2020_10_26_351783 499 22 for for IN 10_1101-2020_10_26_351783 499 23 47 47 CD 10_1101-2020_10_26_351783 499 24 publicly publicly RB 10_1101-2020_10_26_351783 499 25 available available JJ 10_1101-2020_10_26_351783 499 26 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 499 27 datasets dataset NNS 10_1101-2020_10_26_351783 499 28 . . . 10_1101-2020_10_26_351783 500 1 Module module JJ 10_1101-2020_10_26_351783 500 2 performance performance NN 10_1101-2020_10_26_351783 500 3 P p NN 10_1101-2020_10_26_351783 500 4 - - HYPH 10_1101-2020_10_26_351783 500 5 values value NNS 10_1101-2020_10_26_351783 500 6 are be VBP 10_1101-2020_10_26_351783 500 7 shown show VBN 10_1101-2020_10_26_351783 500 8 in in IN 10_1101-2020_10_26_351783 500 9 a a DT 10_1101-2020_10_26_351783 500 10 white white NN 10_1101-2020_10_26_351783 500 11 to to IN 10_1101-2020_10_26_351783 500 12 blue blue JJ 10_1101-2020_10_26_351783 500 13 scale scale NN 10_1101-2020_10_26_351783 500 14 , , , 10_1101-2020_10_26_351783 500 15 where where WRB 10_1101-2020_10_26_351783 500 16 any any DT 10_1101-2020_10_26_351783 500 17 shade shade NN 10_1101-2020_10_26_351783 500 18 of of IN 10_1101-2020_10_26_351783 500 19 blue blue JJ 10_1101-2020_10_26_351783 500 20 represents represent VBZ 10_1101-2020_10_26_351783 500 21 a a DT 10_1101-2020_10_26_351783 500 22 significant significant JJ 10_1101-2020_10_26_351783 500 23 module module NN 10_1101-2020_10_26_351783 500 24 ( ( -LRB- 10_1101-2020_10_26_351783 500 25 < < XX 10_1101-2020_10_26_351783 500 26 0.05 0.05 XX 10_1101-2020_10_26_351783 500 27 ; ; : 10_1101-2020_10_26_351783 500 28 the the DT 10_1101-2020_10_26_351783 500 29 darker darker NN 10_1101-2020_10_26_351783 500 30 , , , 10_1101-2020_10_26_351783 500 31 the the DT 10_1101-2020_10_26_351783 500 32 more more RBR 10_1101-2020_10_26_351783 500 33 significant significant JJ 10_1101-2020_10_26_351783 500 34 ) ) -RRB- 10_1101-2020_10_26_351783 500 35 , , , 10_1101-2020_10_26_351783 500 36 white white NNP 10_1101-2020_10_26_351783 500 37 represents represent VBZ 10_1101-2020_10_26_351783 500 38 a a DT 10_1101-2020_10_26_351783 500 39 non non JJ 10_1101-2020_10_26_351783 500 40 - - JJ 10_1101-2020_10_26_351783 500 41 significant significant JJ 10_1101-2020_10_26_351783 500 42 module module NN 10_1101-2020_10_26_351783 500 43 , , , 10_1101-2020_10_26_351783 500 44 and and CC 10_1101-2020_10_26_351783 500 45 grey grey NNP 10_1101-2020_10_26_351783 500 46 represents represent VBZ 10_1101-2020_10_26_351783 500 47 a a DT 10_1101-2020_10_26_351783 500 48 module module NN 10_1101-2020_10_26_351783 500 49 of of IN 10_1101-2020_10_26_351783 500 50 size size NN 10_1101-2020_10_26_351783 500 51 zero zero CD 10_1101-2020_10_26_351783 500 52 . . . 10_1101-2020_10_26_351783 501 1 Datasets dataset NNS 10_1101-2020_10_26_351783 501 2 are be VBP 10_1101-2020_10_26_351783 501 3 classified classify VBN 10_1101-2020_10_26_351783 501 4 into into IN 10_1101-2020_10_26_351783 501 5 six six CD 10_1101-2020_10_26_351783 501 6 disease disease NN 10_1101-2020_10_26_351783 501 7 types type NNS 10_1101-2020_10_26_351783 501 8 : : : 10_1101-2020_10_26_351783 501 9 cardiovascular cardiovascular NNP 10_1101-2020_10_26_351783 501 10 ( ( -LRB- 10_1101-2020_10_26_351783 501 11 red red NNP 10_1101-2020_10_26_351783 501 12 ) ) -RRB- 10_1101-2020_10_26_351783 501 13 , , , 10_1101-2020_10_26_351783 501 14 glycemic glycemic NNP 10_1101-2020_10_26_351783 501 15 ( ( -LRB- 10_1101-2020_10_26_351783 501 16 golden golden NNP 10_1101-2020_10_26_351783 501 17 ) ) -RRB- 10_1101-2020_10_26_351783 501 18 , , , 10_1101-2020_10_26_351783 501 19 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 501 20 ( ( -LRB- 10_1101-2020_10_26_351783 501 21 green green JJ 10_1101-2020_10_26_351783 501 22 ) ) -RRB- 10_1101-2020_10_26_351783 501 23 , , , 10_1101-2020_10_26_351783 501 24 neurodegenerative neurodegenerative JJ 10_1101-2020_10_26_351783 501 25 ( ( -LRB- 10_1101-2020_10_26_351783 501 26 fuchsia fuchsia NNP 10_1101-2020_10_26_351783 501 27 ) ) -RRB- 10_1101-2020_10_26_351783 501 28 , , , 10_1101-2020_10_26_351783 501 29 psychiatric psychiatric JJ 10_1101-2020_10_26_351783 501 30 and and CC 10_1101-2020_10_26_351783 501 31 social social JJ 10_1101-2020_10_26_351783 501 32 ( ( -LRB- 10_1101-2020_10_26_351783 501 33 pink pink JJ 10_1101-2020_10_26_351783 501 34 ) ) -RRB- 10_1101-2020_10_26_351783 501 35 , , , 10_1101-2020_10_26_351783 501 36 autoimmune autoimmune NNP 10_1101-2020_10_26_351783 501 37 ( ( -LRB- 10_1101-2020_10_26_351783 501 38 dark dark JJ 10_1101-2020_10_26_351783 501 39 purple purple NNP 10_1101-2020_10_26_351783 501 40 ) ) -RRB- 10_1101-2020_10_26_351783 501 41 , , , 10_1101-2020_10_26_351783 501 42 and and CC 10_1101-2020_10_26_351783 501 43 others other NNS 10_1101-2020_10_26_351783 501 44 ( ( -LRB- 10_1101-2020_10_26_351783 501 45 light light JJ 10_1101-2020_10_26_351783 501 46 purple purple NN 10_1101-2020_10_26_351783 501 47 ) ) -RRB- 10_1101-2020_10_26_351783 501 48 ; ; : 10_1101-2020_10_26_351783 501 49 and and CC 10_1101-2020_10_26_351783 501 50 two two CD 10_1101-2020_10_26_351783 501 51 cell cell NN 10_1101-2020_10_26_351783 501 52 types type NNS 10_1101-2020_10_26_351783 501 53 : : : 10_1101-2020_10_26_351783 501 54 blood blood NN 10_1101-2020_10_26_351783 501 55 ( ( -LRB- 10_1101-2020_10_26_351783 501 56 maroon maroon NNP 10_1101-2020_10_26_351783 501 57 ) ) -RRB- 10_1101-2020_10_26_351783 501 58 , , , 10_1101-2020_10_26_351783 501 59 and and CC 10_1101-2020_10_26_351783 501 60 others other NNS 10_1101-2020_10_26_351783 501 61 ( ( -LRB- 10_1101-2020_10_26_351783 501 62 light light JJ 10_1101-2020_10_26_351783 501 63 yellow yellow NN 10_1101-2020_10_26_351783 501 64 ) ) -RRB- 10_1101-2020_10_26_351783 501 65 . . . 10_1101-2020_10_26_351783 502 1 Datasets dataset NNS 10_1101-2020_10_26_351783 502 2 are be VBP 10_1101-2020_10_26_351783 502 3 ranked rank VBN 10_1101-2020_10_26_351783 502 4 by by IN 10_1101-2020_10_26_351783 502 5 meta meta JJ 10_1101-2020_10_26_351783 502 6 P p NN 10_1101-2020_10_26_351783 502 7 - - HYPH 10_1101-2020_10_26_351783 502 8 values value NNS 10_1101-2020_10_26_351783 502 9 using use VBG 10_1101-2020_10_26_351783 502 10 Fisher Fisher NNP 10_1101-2020_10_26_351783 502 11 ’s ’s POS 10_1101-2020_10_26_351783 502 12 method method NN 10_1101-2020_10_26_351783 502 13 of of IN 10_1101-2020_10_26_351783 502 14 the the DT 10_1101-2020_10_26_351783 502 15 single single JJ 10_1101-2020_10_26_351783 502 16 - - HYPH 10_1101-2020_10_26_351783 502 17 method method NN 10_1101-2020_10_26_351783 502 18 module module NN 10_1101-2020_10_26_351783 502 19 P p NN 10_1101-2020_10_26_351783 502 20 - - HYPH 10_1101-2020_10_26_351783 502 21 values value NNS 10_1101-2020_10_26_351783 502 22 across across IN 10_1101-2020_10_26_351783 502 23 and and CC 10_1101-2020_10_26_351783 502 24 within within IN 10_1101-2020_10_26_351783 502 25 their -PRON- PRP$ 10_1101-2020_10_26_351783 502 26 disease disease NN 10_1101-2020_10_26_351783 502 27 types type NNS 10_1101-2020_10_26_351783 502 28 ( ( -LRB- 10_1101-2020_10_26_351783 502 29 dataset dataset NNP 10_1101-2020_10_26_351783 502 30 score score NN 10_1101-2020_10_26_351783 502 31 , , , 10_1101-2020_10_26_351783 502 32 bottom bottom JJ 10_1101-2020_10_26_351783 502 33 boxplot boxplot NN 10_1101-2020_10_26_351783 502 34 ) ) -RRB- 10_1101-2020_10_26_351783 502 35 . . . 10_1101-2020_10_26_351783 503 1 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 503 2 methods method NNS 10_1101-2020_10_26_351783 503 3 are be VBP 10_1101-2020_10_26_351783 503 4 organized organize VBN 10_1101-2020_10_26_351783 503 5 by by IN 10_1101-2020_10_26_351783 503 6 algorithm algorithm NNP 10_1101-2020_10_26_351783 503 7 type type NN 10_1101-2020_10_26_351783 503 8 : : : 10_1101-2020_10_26_351783 503 9 seed seed NN 10_1101-2020_10_26_351783 503 10 - - HYPH 10_1101-2020_10_26_351783 503 11 based base VBN 10_1101-2020_10_26_351783 503 12 ( ( -LRB- 10_1101-2020_10_26_351783 503 13 green green NNP 10_1101-2020_10_26_351783 503 14 ) ) -RRB- 10_1101-2020_10_26_351783 503 15 , , , 10_1101-2020_10_26_351783 503 16 co co NN 10_1101-2020_10_26_351783 503 17 - - NN 10_1101-2020_10_26_351783 503 18 expression expression NN 10_1101-2020_10_26_351783 503 19 - - HYPH 10_1101-2020_10_26_351783 503 20 based base VBN 10_1101-2020_10_26_351783 503 21 ( ( -LRB- 10_1101-2020_10_26_351783 503 22 yellow yellow NNP 10_1101-2020_10_26_351783 503 23 ) ) -RRB- 10_1101-2020_10_26_351783 503 24 , , , 10_1101-2020_10_26_351783 503 25 and and CC 10_1101-2020_10_26_351783 503 26 clique clique NN 10_1101-2020_10_26_351783 503 27 - - HYPH 10_1101-2020_10_26_351783 503 28 based base VBN 10_1101-2020_10_26_351783 503 29 ( ( -LRB- 10_1101-2020_10_26_351783 503 30 red red NNP 10_1101-2020_10_26_351783 503 31 ) ) -RRB- 10_1101-2020_10_26_351783 503 32 , , , 10_1101-2020_10_26_351783 503 33 plus plus CC 10_1101-2020_10_26_351783 503 34 the the DT 10_1101-2020_10_26_351783 503 35 consensus consensus NN 10_1101-2020_10_26_351783 503 36 modules module NNS 10_1101-2020_10_26_351783 503 37 ( ( -LRB- 10_1101-2020_10_26_351783 503 38 blue blue NNP 10_1101-2020_10_26_351783 503 39 ) ) -RRB- 10_1101-2020_10_26_351783 503 40 . . . 10_1101-2020_10_26_351783 504 1 Single single JJ 10_1101-2020_10_26_351783 504 2 - - HYPH 10_1101-2020_10_26_351783 504 3 methods method NNS 10_1101-2020_10_26_351783 504 4 and and CC 10_1101-2020_10_26_351783 504 5 consensus consensus NN 10_1101-2020_10_26_351783 504 6 were be VBD 10_1101-2020_10_26_351783 504 7 scored score VBN 10_1101-2020_10_26_351783 504 8 by by IN 10_1101-2020_10_26_351783 504 9 meta meta JJ 10_1101-2020_10_26_351783 504 10 P p NN 10_1101-2020_10_26_351783 504 11 - - HYPH 10_1101-2020_10_26_351783 504 12 values value NNS 10_1101-2020_10_26_351783 504 13 across across IN 10_1101-2020_10_26_351783 504 14 ( ( -LRB- 10_1101-2020_10_26_351783 504 15 which which WDT 10_1101-2020_10_26_351783 504 16 was be VBD 10_1101-2020_10_26_351783 504 17 not not RB 10_1101-2020_10_26_351783 504 18 certified certify VBN 10_1101-2020_10_26_351783 504 19 by by IN 10_1101-2020_10_26_351783 504 20 peer peer NN 10_1101-2020_10_26_351783 504 21 review review NN 10_1101-2020_10_26_351783 504 22 ) ) -RRB- 10_1101-2020_10_26_351783 504 23 is be VBZ 10_1101-2020_10_26_351783 504 24 the the DT 10_1101-2020_10_26_351783 504 25 author author NN 10_1101-2020_10_26_351783 504 26 / / SYM 10_1101-2020_10_26_351783 504 27 funder funder NN 10_1101-2020_10_26_351783 504 28 . . . 10_1101-2020_10_26_351783 505 1 All all DT 10_1101-2020_10_26_351783 505 2 rights right NNS 10_1101-2020_10_26_351783 505 3 reserved reserve VBD 10_1101-2020_10_26_351783 505 4 . . . 10_1101-2020_10_26_351783 506 1 No no DT 10_1101-2020_10_26_351783 506 2 reuse reuse NN 10_1101-2020_10_26_351783 506 3 allowed allow VBN 10_1101-2020_10_26_351783 506 4 without without IN 10_1101-2020_10_26_351783 506 5 permission permission NN 10_1101-2020_10_26_351783 506 6 . . . 10_1101-2020_10_26_351783 507 1 The the DT 10_1101-2020_10_26_351783 507 2 copyright copyright NN 10_1101-2020_10_26_351783 507 3 holder holder NN 10_1101-2020_10_26_351783 507 4 for for IN 10_1101-2020_10_26_351783 507 5 this this DT 10_1101-2020_10_26_351783 507 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 507 7 version version NN 10_1101-2020_10_26_351783 507 8 posted post VBD 10_1101-2020_10_26_351783 507 9 January January NNP 10_1101-2020_10_26_351783 507 10 6 6 CD 10_1101-2020_10_26_351783 507 11 , , , 10_1101-2020_10_26_351783 507 12 2021 2021 CD 10_1101-2020_10_26_351783 507 13 . . . 10_1101-2020_10_26_351783 507 14 ; ; : 10_1101-2020_10_26_351783 507 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 507 16 : : : 10_1101-2020_10_26_351783 507 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 507 18 preprint preprint NN 10_1101-2020_10_26_351783 507 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 507 20 28 28 CD 10_1101-2020_10_26_351783 507 21 datasets dataset NNS 10_1101-2020_10_26_351783 507 22 ( ( -LRB- 10_1101-2020_10_26_351783 507 23 method method NN 10_1101-2020_10_26_351783 507 24 score score NN 10_1101-2020_10_26_351783 507 25 , , , 10_1101-2020_10_26_351783 507 26 right right JJ 10_1101-2020_10_26_351783 507 27 boxplot boxplot NN 10_1101-2020_10_26_351783 507 28 ) ) -RRB- 10_1101-2020_10_26_351783 507 29 . . . 10_1101-2020_10_26_351783 508 1 Consensus Consensus NNP 10_1101-2020_10_26_351783 508 2 x/8 x/8 NN 10_1101-2020_10_26_351783 508 3 indicates indicate VBZ 10_1101-2020_10_26_351783 508 4 that that IN 10_1101-2020_10_26_351783 508 5 the the DT 10_1101-2020_10_26_351783 508 6 module module JJ 10_1101-2020_10_26_351783 508 7 genes gene NNS 10_1101-2020_10_26_351783 508 8 are be VBP 10_1101-2020_10_26_351783 508 9 found find VBN 10_1101-2020_10_26_351783 508 10 in in IN 10_1101-2020_10_26_351783 508 11 at at IN 10_1101-2020_10_26_351783 508 12 least least JJS 10_1101-2020_10_26_351783 508 13 x x DT 10_1101-2020_10_26_351783 508 14 methods method NNS 10_1101-2020_10_26_351783 508 15 out out IN 10_1101-2020_10_26_351783 508 16 of of IN 10_1101-2020_10_26_351783 508 17 eight eight CD 10_1101-2020_10_26_351783 508 18 . . . 10_1101-2020_10_26_351783 509 1 ( ( -LRB- 10_1101-2020_10_26_351783 509 2 b b LS 10_1101-2020_10_26_351783 509 3 ) ) -RRB- 10_1101-2020_10_26_351783 509 4 Scatter scatter NN 10_1101-2020_10_26_351783 509 5 plot plot NN 10_1101-2020_10_26_351783 509 6 showing show VBG 10_1101-2020_10_26_351783 509 7 Spearman spearman NN 10_1101-2020_10_26_351783 509 8 correlation correlation NN 10_1101-2020_10_26_351783 509 9 between between IN 10_1101-2020_10_26_351783 509 10 module module JJ 10_1101-2020_10_26_351783 509 11 score score NN 10_1101-2020_10_26_351783 509 12 and and CC 10_1101-2020_10_26_351783 509 13 betweenness betweenness JJ 10_1101-2020_10_26_351783 509 14 centrality centrality NN 10_1101-2020_10_26_351783 509 15 . . . 10_1101-2020_10_26_351783 510 1 Modules module NNS 10_1101-2020_10_26_351783 510 2 are be VBP 10_1101-2020_10_26_351783 510 3 represented represent VBN 10_1101-2020_10_26_351783 510 4 with with IN 10_1101-2020_10_26_351783 510 5 a a DT 10_1101-2020_10_26_351783 510 6 different different JJ 10_1101-2020_10_26_351783 510 7 shape shape NN 10_1101-2020_10_26_351783 510 8 depending depend VBG 10_1101-2020_10_26_351783 510 9 on on IN 10_1101-2020_10_26_351783 510 10 their -PRON- PRP$ 10_1101-2020_10_26_351783 510 11 method method NN 10_1101-2020_10_26_351783 510 12 and and CC 10_1101-2020_10_26_351783 510 13 colored color VBN 10_1101-2020_10_26_351783 510 14 based base VBN 10_1101-2020_10_26_351783 510 15 on on IN 10_1101-2020_10_26_351783 510 16 the the DT 10_1101-2020_10_26_351783 510 17 disease disease NN 10_1101-2020_10_26_351783 510 18 type type NN 10_1101-2020_10_26_351783 510 19 . . . 10_1101-2020_10_26_351783 511 1 ( ( -LRB- 10_1101-2020_10_26_351783 511 2 c c NN 10_1101-2020_10_26_351783 511 3 ) ) -RRB- 10_1101-2020_10_26_351783 511 4 Scatter scatter NN 10_1101-2020_10_26_351783 511 5 plot plot NN 10_1101-2020_10_26_351783 511 6 showing show VBG 10_1101-2020_10_26_351783 511 7 Spearman spearman NN 10_1101-2020_10_26_351783 511 8 correlation correlation NN 10_1101-2020_10_26_351783 511 9 between between IN 10_1101-2020_10_26_351783 511 10 module module JJ 10_1101-2020_10_26_351783 511 11 score score NN 10_1101-2020_10_26_351783 511 12 and and CC 10_1101-2020_10_26_351783 511 13 module module JJ 10_1101-2020_10_26_351783 511 14 size size NN 10_1101-2020_10_26_351783 511 15 . . . 10_1101-2020_10_26_351783 512 1 Modules module NNS 10_1101-2020_10_26_351783 512 2 are be VBP 10_1101-2020_10_26_351783 512 3 represented represent VBN 10_1101-2020_10_26_351783 512 4 with with IN 10_1101-2020_10_26_351783 512 5 a a DT 10_1101-2020_10_26_351783 512 6 different different JJ 10_1101-2020_10_26_351783 512 7 shape shape NN 10_1101-2020_10_26_351783 512 8 depending depend VBG 10_1101-2020_10_26_351783 512 9 on on IN 10_1101-2020_10_26_351783 512 10 their -PRON- PRP$ 10_1101-2020_10_26_351783 512 11 method method NN 10_1101-2020_10_26_351783 512 12 and and CC 10_1101-2020_10_26_351783 512 13 colored color VBN 10_1101-2020_10_26_351783 512 14 based base VBN 10_1101-2020_10_26_351783 512 15 on on IN 10_1101-2020_10_26_351783 512 16 the the DT 10_1101-2020_10_26_351783 512 17 disease disease NN 10_1101-2020_10_26_351783 512 18 type type NN 10_1101-2020_10_26_351783 512 19 . . . 10_1101-2020_10_26_351783 513 1 ( ( -LRB- 10_1101-2020_10_26_351783 513 2 which which WDT 10_1101-2020_10_26_351783 513 3 was be VBD 10_1101-2020_10_26_351783 513 4 not not RB 10_1101-2020_10_26_351783 513 5 certified certify VBN 10_1101-2020_10_26_351783 513 6 by by IN 10_1101-2020_10_26_351783 513 7 peer peer NN 10_1101-2020_10_26_351783 513 8 review review NN 10_1101-2020_10_26_351783 513 9 ) ) -RRB- 10_1101-2020_10_26_351783 513 10 is be VBZ 10_1101-2020_10_26_351783 513 11 the the DT 10_1101-2020_10_26_351783 513 12 author author NN 10_1101-2020_10_26_351783 513 13 / / SYM 10_1101-2020_10_26_351783 513 14 funder funder NN 10_1101-2020_10_26_351783 513 15 . . . 10_1101-2020_10_26_351783 514 1 All all DT 10_1101-2020_10_26_351783 514 2 rights right NNS 10_1101-2020_10_26_351783 514 3 reserved reserve VBD 10_1101-2020_10_26_351783 514 4 . . . 10_1101-2020_10_26_351783 515 1 No no DT 10_1101-2020_10_26_351783 515 2 reuse reuse NN 10_1101-2020_10_26_351783 515 3 allowed allow VBN 10_1101-2020_10_26_351783 515 4 without without IN 10_1101-2020_10_26_351783 515 5 permission permission NN 10_1101-2020_10_26_351783 515 6 . . . 10_1101-2020_10_26_351783 516 1 The the DT 10_1101-2020_10_26_351783 516 2 copyright copyright NN 10_1101-2020_10_26_351783 516 3 holder holder NN 10_1101-2020_10_26_351783 516 4 for for IN 10_1101-2020_10_26_351783 516 5 this this DT 10_1101-2020_10_26_351783 516 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 516 7 version version NN 10_1101-2020_10_26_351783 516 8 posted post VBD 10_1101-2020_10_26_351783 516 9 January January NNP 10_1101-2020_10_26_351783 516 10 6 6 CD 10_1101-2020_10_26_351783 516 11 , , , 10_1101-2020_10_26_351783 516 12 2021 2021 CD 10_1101-2020_10_26_351783 516 13 . . . 10_1101-2020_10_26_351783 516 14 ; ; : 10_1101-2020_10_26_351783 516 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 516 16 : : : 10_1101-2020_10_26_351783 516 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 516 18 preprint preprint NN 10_1101-2020_10_26_351783 516 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 516 20 Figure figure NN 10_1101-2020_10_26_351783 516 21 3 3 CD 10_1101-2020_10_26_351783 516 22 . . . 10_1101-2020_10_26_351783 517 1 Genomic genomic JJ 10_1101-2020_10_26_351783 517 2 concordance concordance NN 10_1101-2020_10_26_351783 517 3 of of IN 10_1101-2020_10_26_351783 517 4 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 517 5 modules module NNS 10_1101-2020_10_26_351783 517 6 on on IN 10_1101-2020_10_26_351783 517 7 methylomic methylomic JJ 10_1101-2020_10_26_351783 517 8 datasets dataset NNS 10_1101-2020_10_26_351783 517 9 . . . 10_1101-2020_10_26_351783 518 1 ( ( -LRB- 10_1101-2020_10_26_351783 518 2 a a DT 10_1101-2020_10_26_351783 518 3 ) ) -RRB- 10_1101-2020_10_26_351783 518 4 Heatmap Heatmap NNP 10_1101-2020_10_26_351783 518 5 of of IN 10_1101-2020_10_26_351783 518 6 Pascal Pascal NNP 10_1101-2020_10_26_351783 518 7 p p NN 10_1101-2020_10_26_351783 518 8 - - HYPH 10_1101-2020_10_26_351783 518 9 values value NNS 10_1101-2020_10_26_351783 518 10 for for IN 10_1101-2020_10_26_351783 518 11 eight eight CD 10_1101-2020_10_26_351783 518 12 single single JJ 10_1101-2020_10_26_351783 518 13 - - HYPH 10_1101-2020_10_26_351783 518 14 method method NN 10_1101-2020_10_26_351783 518 15 and and CC 10_1101-2020_10_26_351783 518 16 eight eight CD 10_1101-2020_10_26_351783 518 17 consensus consensus NN 10_1101-2020_10_26_351783 518 18 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 518 19 modules modules NNP 10_1101-2020_10_26_351783 518 20 , , , 10_1101-2020_10_26_351783 518 21 identified identify VBN 10_1101-2020_10_26_351783 518 22 for for IN 10_1101-2020_10_26_351783 518 23 ten ten CD 10_1101-2020_10_26_351783 518 24 publicly publicly RB 10_1101-2020_10_26_351783 518 25 available available JJ 10_1101-2020_10_26_351783 518 26 methylomic methylomic JJ 10_1101-2020_10_26_351783 518 27 datasets dataset NNS 10_1101-2020_10_26_351783 518 28 . . . 10_1101-2020_10_26_351783 519 1 Module module JJ 10_1101-2020_10_26_351783 519 2 performance performance NN 10_1101-2020_10_26_351783 519 3 P p NN 10_1101-2020_10_26_351783 519 4 - - HYPH 10_1101-2020_10_26_351783 519 5 values value NNS 10_1101-2020_10_26_351783 519 6 are be VBP 10_1101-2020_10_26_351783 519 7 shown show VBN 10_1101-2020_10_26_351783 519 8 in in IN 10_1101-2020_10_26_351783 519 9 a a DT 10_1101-2020_10_26_351783 519 10 white white NN 10_1101-2020_10_26_351783 519 11 to to IN 10_1101-2020_10_26_351783 519 12 blue blue JJ 10_1101-2020_10_26_351783 519 13 scale scale NN 10_1101-2020_10_26_351783 519 14 , , , 10_1101-2020_10_26_351783 519 15 where where WRB 10_1101-2020_10_26_351783 519 16 any any DT 10_1101-2020_10_26_351783 519 17 shade shade NN 10_1101-2020_10_26_351783 519 18 of of IN 10_1101-2020_10_26_351783 519 19 blue blue JJ 10_1101-2020_10_26_351783 519 20 represents represent VBZ 10_1101-2020_10_26_351783 519 21 a a DT 10_1101-2020_10_26_351783 519 22 significant significant JJ 10_1101-2020_10_26_351783 519 23 module module NN 10_1101-2020_10_26_351783 519 24 ( ( -LRB- 10_1101-2020_10_26_351783 519 25 P p NN 10_1101-2020_10_26_351783 519 26 < < XX 10_1101-2020_10_26_351783 519 27 0.05 0.05 XX 10_1101-2020_10_26_351783 519 28 ; ; : 10_1101-2020_10_26_351783 519 29 the the DT 10_1101-2020_10_26_351783 519 30 darker darker NN 10_1101-2020_10_26_351783 519 31 , , , 10_1101-2020_10_26_351783 519 32 the the DT 10_1101-2020_10_26_351783 519 33 more more RBR 10_1101-2020_10_26_351783 519 34 significant significant JJ 10_1101-2020_10_26_351783 519 35 ) ) -RRB- 10_1101-2020_10_26_351783 519 36 , , , 10_1101-2020_10_26_351783 519 37 white white NNP 10_1101-2020_10_26_351783 519 38 represents represent VBZ 10_1101-2020_10_26_351783 519 39 a a DT 10_1101-2020_10_26_351783 519 40 non non JJ 10_1101-2020_10_26_351783 519 41 - - JJ 10_1101-2020_10_26_351783 519 42 significant significant JJ 10_1101-2020_10_26_351783 519 43 module module NN 10_1101-2020_10_26_351783 519 44 , , , 10_1101-2020_10_26_351783 519 45 and and CC 10_1101-2020_10_26_351783 519 46 grey grey NNP 10_1101-2020_10_26_351783 519 47 represents represent VBZ 10_1101-2020_10_26_351783 519 48 a a DT 10_1101-2020_10_26_351783 519 49 module module NN 10_1101-2020_10_26_351783 519 50 of of IN 10_1101-2020_10_26_351783 519 51 size size NN 10_1101-2020_10_26_351783 519 52 zero zero CD 10_1101-2020_10_26_351783 519 53 . . . 10_1101-2020_10_26_351783 520 1 Datasets dataset NNS 10_1101-2020_10_26_351783 520 2 are be VBP 10_1101-2020_10_26_351783 520 3 classified classify VBN 10_1101-2020_10_26_351783 520 4 into into IN 10_1101-2020_10_26_351783 520 5 two two CD 10_1101-2020_10_26_351783 520 6 disease disease NN 10_1101-2020_10_26_351783 520 7 types type NNS 10_1101-2020_10_26_351783 520 8 : : : 10_1101-2020_10_26_351783 520 9 glycemic glycemic NNP 10_1101-2020_10_26_351783 520 10 ( ( -LRB- 10_1101-2020_10_26_351783 520 11 golden golden NNP 10_1101-2020_10_26_351783 520 12 ) ) -RRB- 10_1101-2020_10_26_351783 520 13 , , , 10_1101-2020_10_26_351783 520 14 and and CC 10_1101-2020_10_26_351783 520 15 inflammatory inflammatory JJ 10_1101-2020_10_26_351783 520 16 ( ( -LRB- 10_1101-2020_10_26_351783 520 17 green green JJ 10_1101-2020_10_26_351783 520 18 ) ) -RRB- 10_1101-2020_10_26_351783 520 19 ; ; : 10_1101-2020_10_26_351783 520 20 and and CC 10_1101-2020_10_26_351783 520 21 two two CD 10_1101-2020_10_26_351783 520 22 cell cell NN 10_1101-2020_10_26_351783 520 23 types type NNS 10_1101-2020_10_26_351783 520 24 : : : 10_1101-2020_10_26_351783 520 25 blood blood NN 10_1101-2020_10_26_351783 520 26 ( ( -LRB- 10_1101-2020_10_26_351783 520 27 maroon maroon NNP 10_1101-2020_10_26_351783 520 28 ) ) -RRB- 10_1101-2020_10_26_351783 520 29 , , , 10_1101-2020_10_26_351783 520 30 and and CC 10_1101-2020_10_26_351783 520 31 others other NNS 10_1101-2020_10_26_351783 520 32 ( ( -LRB- 10_1101-2020_10_26_351783 520 33 light light JJ 10_1101-2020_10_26_351783 520 34 yellow yellow NN 10_1101-2020_10_26_351783 520 35 ) ) -RRB- 10_1101-2020_10_26_351783 520 36 . . . 10_1101-2020_10_26_351783 521 1 Datasets dataset NNS 10_1101-2020_10_26_351783 521 2 are be VBP 10_1101-2020_10_26_351783 521 3 ranked rank VBN 10_1101-2020_10_26_351783 521 4 by by IN 10_1101-2020_10_26_351783 521 5 Fisher Fisher NNP 10_1101-2020_10_26_351783 521 6 ’s ’s POS 10_1101-2020_10_26_351783 521 7 combined combine VBN 10_1101-2020_10_26_351783 521 8 P p NN 10_1101-2020_10_26_351783 521 9 of of IN 10_1101-2020_10_26_351783 521 10 the the DT 10_1101-2020_10_26_351783 521 11 single single JJ 10_1101-2020_10_26_351783 521 12 - - HYPH 10_1101-2020_10_26_351783 521 13 method method NN 10_1101-2020_10_26_351783 521 14 module module NN 10_1101-2020_10_26_351783 521 15 P p NN 10_1101-2020_10_26_351783 521 16 - - HYPH 10_1101-2020_10_26_351783 521 17 values value NNS 10_1101-2020_10_26_351783 521 18 across across IN 10_1101-2020_10_26_351783 521 19 and and CC 10_1101-2020_10_26_351783 521 20 within within IN 10_1101-2020_10_26_351783 521 21 their -PRON- PRP$ 10_1101-2020_10_26_351783 521 22 disease disease NN 10_1101-2020_10_26_351783 521 23 types type NNS 10_1101-2020_10_26_351783 521 24 ( ( -LRB- 10_1101-2020_10_26_351783 521 25 dataset dataset NNP 10_1101-2020_10_26_351783 521 26 score score NN 10_1101-2020_10_26_351783 521 27 , , , 10_1101-2020_10_26_351783 521 28 bottom bottom JJ 10_1101-2020_10_26_351783 521 29 boxplot boxplot NN 10_1101-2020_10_26_351783 521 30 ) ) -RRB- 10_1101-2020_10_26_351783 521 31 . . . 10_1101-2020_10_26_351783 522 1 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 522 2 methods method NNS 10_1101-2020_10_26_351783 522 3 are be VBP 10_1101-2020_10_26_351783 522 4 organized organize VBN 10_1101-2020_10_26_351783 522 5 by by IN 10_1101-2020_10_26_351783 522 6 algorithm algorithm NNP 10_1101-2020_10_26_351783 522 7 type type NN 10_1101-2020_10_26_351783 522 8 : : : 10_1101-2020_10_26_351783 522 9 seed seed NN 10_1101-2020_10_26_351783 522 10 - - HYPH 10_1101-2020_10_26_351783 522 11 based base VBN 10_1101-2020_10_26_351783 522 12 ( ( -LRB- 10_1101-2020_10_26_351783 522 13 green green NNP 10_1101-2020_10_26_351783 522 14 ) ) -RRB- 10_1101-2020_10_26_351783 522 15 , , , 10_1101-2020_10_26_351783 522 16 co co JJ 10_1101-2020_10_26_351783 522 17 - - NN 10_1101-2020_10_26_351783 522 18 expression- expression- JJ 10_1101-2020_10_26_351783 522 19 based base VBN 10_1101-2020_10_26_351783 522 20 ( ( -LRB- 10_1101-2020_10_26_351783 522 21 yellow yellow NNP 10_1101-2020_10_26_351783 522 22 ) ) -RRB- 10_1101-2020_10_26_351783 522 23 , , , 10_1101-2020_10_26_351783 522 24 and and CC 10_1101-2020_10_26_351783 522 25 clique clique NN 10_1101-2020_10_26_351783 522 26 - - HYPH 10_1101-2020_10_26_351783 522 27 based base VBN 10_1101-2020_10_26_351783 522 28 ( ( -LRB- 10_1101-2020_10_26_351783 522 29 red red NNP 10_1101-2020_10_26_351783 522 30 ) ) -RRB- 10_1101-2020_10_26_351783 522 31 , , , 10_1101-2020_10_26_351783 522 32 plus plus CC 10_1101-2020_10_26_351783 522 33 the the DT 10_1101-2020_10_26_351783 522 34 consensus consensus NN 10_1101-2020_10_26_351783 522 35 modules module NNS 10_1101-2020_10_26_351783 522 36 ( ( -LRB- 10_1101-2020_10_26_351783 522 37 blue blue NNP 10_1101-2020_10_26_351783 522 38 ) ) -RRB- 10_1101-2020_10_26_351783 522 39 . . . 10_1101-2020_10_26_351783 523 1 Single single JJ 10_1101-2020_10_26_351783 523 2 - - HYPH 10_1101-2020_10_26_351783 523 3 methods method NNS 10_1101-2020_10_26_351783 523 4 and and CC 10_1101-2020_10_26_351783 523 5 consensus consensus NN 10_1101-2020_10_26_351783 523 6 are be VBP 10_1101-2020_10_26_351783 523 7 scored score VBN 10_1101-2020_10_26_351783 523 8 by by IN 10_1101-2020_10_26_351783 523 9 meta meta JJ 10_1101-2020_10_26_351783 523 10 P p NN 10_1101-2020_10_26_351783 523 11 - - HYPH 10_1101-2020_10_26_351783 523 12 values value NNS 10_1101-2020_10_26_351783 523 13 across across IN 10_1101-2020_10_26_351783 523 14 datasets dataset NNS 10_1101-2020_10_26_351783 523 15 ( ( -LRB- 10_1101-2020_10_26_351783 523 16 method method NN 10_1101-2020_10_26_351783 523 17 score score NN 10_1101-2020_10_26_351783 523 18 , , , 10_1101-2020_10_26_351783 523 19 right right JJ 10_1101-2020_10_26_351783 523 20 boxplot boxplot NN 10_1101-2020_10_26_351783 523 21 ) ) -RRB- 10_1101-2020_10_26_351783 523 22 . . . 10_1101-2020_10_26_351783 524 1 Consensus Consensus NNP 10_1101-2020_10_26_351783 524 2 x/8 x/8 NN 10_1101-2020_10_26_351783 524 3 indicates indicate VBZ 10_1101-2020_10_26_351783 524 4 that that IN 10_1101-2020_10_26_351783 524 5 the the DT 10_1101-2020_10_26_351783 524 6 module module JJ 10_1101-2020_10_26_351783 524 7 genes gene NNS 10_1101-2020_10_26_351783 524 8 are be VBP 10_1101-2020_10_26_351783 524 9 found find VBN 10_1101-2020_10_26_351783 524 10 in in IN 10_1101-2020_10_26_351783 524 11 at at IN 10_1101-2020_10_26_351783 524 12 least least JJS 10_1101-2020_10_26_351783 524 13 x x DT 10_1101-2020_10_26_351783 524 14 methods method NNS 10_1101-2020_10_26_351783 524 15 out out IN 10_1101-2020_10_26_351783 524 16 of of IN 10_1101-2020_10_26_351783 524 17 eight eight CD 10_1101-2020_10_26_351783 524 18 . . . 10_1101-2020_10_26_351783 525 1 ( ( -LRB- 10_1101-2020_10_26_351783 525 2 b b LS 10_1101-2020_10_26_351783 525 3 ) ) -RRB- 10_1101-2020_10_26_351783 525 4 Scatter scatter NN 10_1101-2020_10_26_351783 525 5 plot plot NN 10_1101-2020_10_26_351783 525 6 ( ( -LRB- 10_1101-2020_10_26_351783 525 7 which which WDT 10_1101-2020_10_26_351783 525 8 was be VBD 10_1101-2020_10_26_351783 525 9 not not RB 10_1101-2020_10_26_351783 525 10 certified certify VBN 10_1101-2020_10_26_351783 525 11 by by IN 10_1101-2020_10_26_351783 525 12 peer peer NN 10_1101-2020_10_26_351783 525 13 review review NN 10_1101-2020_10_26_351783 525 14 ) ) -RRB- 10_1101-2020_10_26_351783 525 15 is be VBZ 10_1101-2020_10_26_351783 525 16 the the DT 10_1101-2020_10_26_351783 525 17 author author NN 10_1101-2020_10_26_351783 525 18 / / SYM 10_1101-2020_10_26_351783 525 19 funder funder NN 10_1101-2020_10_26_351783 525 20 . . . 10_1101-2020_10_26_351783 526 1 All all DT 10_1101-2020_10_26_351783 526 2 rights right NNS 10_1101-2020_10_26_351783 526 3 reserved reserve VBD 10_1101-2020_10_26_351783 526 4 . . . 10_1101-2020_10_26_351783 527 1 No no DT 10_1101-2020_10_26_351783 527 2 reuse reuse NN 10_1101-2020_10_26_351783 527 3 allowed allow VBN 10_1101-2020_10_26_351783 527 4 without without IN 10_1101-2020_10_26_351783 527 5 permission permission NN 10_1101-2020_10_26_351783 527 6 . . . 10_1101-2020_10_26_351783 528 1 The the DT 10_1101-2020_10_26_351783 528 2 copyright copyright NN 10_1101-2020_10_26_351783 528 3 holder holder NN 10_1101-2020_10_26_351783 528 4 for for IN 10_1101-2020_10_26_351783 528 5 this this DT 10_1101-2020_10_26_351783 528 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 528 7 version version NN 10_1101-2020_10_26_351783 528 8 posted post VBD 10_1101-2020_10_26_351783 528 9 January January NNP 10_1101-2020_10_26_351783 528 10 6 6 CD 10_1101-2020_10_26_351783 528 11 , , , 10_1101-2020_10_26_351783 528 12 2021 2021 CD 10_1101-2020_10_26_351783 528 13 . . . 10_1101-2020_10_26_351783 528 14 ; ; : 10_1101-2020_10_26_351783 528 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 528 16 : : : 10_1101-2020_10_26_351783 528 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 528 18 preprint preprint NN 10_1101-2020_10_26_351783 528 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 528 20 30 30 CD 10_1101-2020_10_26_351783 528 21 showing show VBG 10_1101-2020_10_26_351783 528 22 Spearman Spearman NNP 10_1101-2020_10_26_351783 528 23 correlation correlation NN 10_1101-2020_10_26_351783 528 24 between between IN 10_1101-2020_10_26_351783 528 25 module module JJ 10_1101-2020_10_26_351783 528 26 score score NN 10_1101-2020_10_26_351783 528 27 and and CC 10_1101-2020_10_26_351783 528 28 betweenness betweenness JJ 10_1101-2020_10_26_351783 528 29 centrality centrality NN 10_1101-2020_10_26_351783 528 30 . . . 10_1101-2020_10_26_351783 529 1 Modules module NNS 10_1101-2020_10_26_351783 529 2 are be VBP 10_1101-2020_10_26_351783 529 3 represented represent VBN 10_1101-2020_10_26_351783 529 4 with with IN 10_1101-2020_10_26_351783 529 5 a a DT 10_1101-2020_10_26_351783 529 6 different different JJ 10_1101-2020_10_26_351783 529 7 shape shape NN 10_1101-2020_10_26_351783 529 8 depending depend VBG 10_1101-2020_10_26_351783 529 9 on on IN 10_1101-2020_10_26_351783 529 10 their -PRON- PRP$ 10_1101-2020_10_26_351783 529 11 method method NN 10_1101-2020_10_26_351783 529 12 and and CC 10_1101-2020_10_26_351783 529 13 colored color VBN 10_1101-2020_10_26_351783 529 14 based base VBN 10_1101-2020_10_26_351783 529 15 on on IN 10_1101-2020_10_26_351783 529 16 the the DT 10_1101-2020_10_26_351783 529 17 disease disease NN 10_1101-2020_10_26_351783 529 18 type type NN 10_1101-2020_10_26_351783 529 19 . . . 10_1101-2020_10_26_351783 530 1 ( ( -LRB- 10_1101-2020_10_26_351783 530 2 c c NN 10_1101-2020_10_26_351783 530 3 ) ) -RRB- 10_1101-2020_10_26_351783 530 4 Scatter scatter NN 10_1101-2020_10_26_351783 530 5 plot plot NN 10_1101-2020_10_26_351783 530 6 showing show VBG 10_1101-2020_10_26_351783 530 7 Spearman spearman NN 10_1101-2020_10_26_351783 530 8 correlation correlation NN 10_1101-2020_10_26_351783 530 9 between between IN 10_1101-2020_10_26_351783 530 10 module module JJ 10_1101-2020_10_26_351783 530 11 score score NN 10_1101-2020_10_26_351783 530 12 and and CC 10_1101-2020_10_26_351783 530 13 module module JJ 10_1101-2020_10_26_351783 530 14 size size NN 10_1101-2020_10_26_351783 530 15 . . . 10_1101-2020_10_26_351783 531 1 Modules module NNS 10_1101-2020_10_26_351783 531 2 are be VBP 10_1101-2020_10_26_351783 531 3 represented represent VBN 10_1101-2020_10_26_351783 531 4 with with IN 10_1101-2020_10_26_351783 531 5 a a DT 10_1101-2020_10_26_351783 531 6 different different JJ 10_1101-2020_10_26_351783 531 7 shape shape NN 10_1101-2020_10_26_351783 531 8 depending depend VBG 10_1101-2020_10_26_351783 531 9 on on IN 10_1101-2020_10_26_351783 531 10 their -PRON- PRP$ 10_1101-2020_10_26_351783 531 11 method method NN 10_1101-2020_10_26_351783 531 12 and and CC 10_1101-2020_10_26_351783 531 13 colored color VBN 10_1101-2020_10_26_351783 531 14 based base VBN 10_1101-2020_10_26_351783 531 15 on on IN 10_1101-2020_10_26_351783 531 16 the the DT 10_1101-2020_10_26_351783 531 17 disease disease NN 10_1101-2020_10_26_351783 531 18 type type NN 10_1101-2020_10_26_351783 531 19 . . . 10_1101-2020_10_26_351783 532 1 ( ( -LRB- 10_1101-2020_10_26_351783 532 2 which which WDT 10_1101-2020_10_26_351783 532 3 was be VBD 10_1101-2020_10_26_351783 532 4 not not RB 10_1101-2020_10_26_351783 532 5 certified certify VBN 10_1101-2020_10_26_351783 532 6 by by IN 10_1101-2020_10_26_351783 532 7 peer peer NN 10_1101-2020_10_26_351783 532 8 review review NN 10_1101-2020_10_26_351783 532 9 ) ) -RRB- 10_1101-2020_10_26_351783 532 10 is be VBZ 10_1101-2020_10_26_351783 532 11 the the DT 10_1101-2020_10_26_351783 532 12 author author NN 10_1101-2020_10_26_351783 532 13 / / SYM 10_1101-2020_10_26_351783 532 14 funder funder NN 10_1101-2020_10_26_351783 532 15 . . . 10_1101-2020_10_26_351783 533 1 All all DT 10_1101-2020_10_26_351783 533 2 rights right NNS 10_1101-2020_10_26_351783 533 3 reserved reserve VBD 10_1101-2020_10_26_351783 533 4 . . . 10_1101-2020_10_26_351783 534 1 No no DT 10_1101-2020_10_26_351783 534 2 reuse reuse NN 10_1101-2020_10_26_351783 534 3 allowed allow VBN 10_1101-2020_10_26_351783 534 4 without without IN 10_1101-2020_10_26_351783 534 5 permission permission NN 10_1101-2020_10_26_351783 534 6 . . . 10_1101-2020_10_26_351783 535 1 The the DT 10_1101-2020_10_26_351783 535 2 copyright copyright NN 10_1101-2020_10_26_351783 535 3 holder holder NN 10_1101-2020_10_26_351783 535 4 for for IN 10_1101-2020_10_26_351783 535 5 this this DT 10_1101-2020_10_26_351783 535 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 535 7 version version NN 10_1101-2020_10_26_351783 535 8 posted post VBD 10_1101-2020_10_26_351783 535 9 January January NNP 10_1101-2020_10_26_351783 535 10 6 6 CD 10_1101-2020_10_26_351783 535 11 , , , 10_1101-2020_10_26_351783 535 12 2021 2021 CD 10_1101-2020_10_26_351783 535 13 . . . 10_1101-2020_10_26_351783 535 14 ; ; : 10_1101-2020_10_26_351783 535 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 535 16 : : : 10_1101-2020_10_26_351783 535 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 535 18 preprint preprint NN 10_1101-2020_10_26_351783 535 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 535 20 31 31 CD 10_1101-2020_10_26_351783 535 21 Figure figure NN 10_1101-2020_10_26_351783 535 22 4 4 CD 10_1101-2020_10_26_351783 535 23 . . . 10_1101-2020_10_26_351783 536 1 Genomic genomic JJ 10_1101-2020_10_26_351783 536 2 concordance concordance NN 10_1101-2020_10_26_351783 536 3 of of IN 10_1101-2020_10_26_351783 536 4 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 536 5 modules module NNS 10_1101-2020_10_26_351783 536 6 on on IN 10_1101-2020_10_26_351783 536 7 MS MS NNP 10_1101-2020_10_26_351783 536 8 use use VBP 10_1101-2020_10_26_351783 536 9 case case NN 10_1101-2020_10_26_351783 536 10 data datum NNS 10_1101-2020_10_26_351783 536 11 . . . 10_1101-2020_10_26_351783 537 1 ( ( -LRB- 10_1101-2020_10_26_351783 537 2 a a DT 10_1101-2020_10_26_351783 537 3 ) ) -RRB- 10_1101-2020_10_26_351783 537 4 Heatmap Heatmap NNP 10_1101-2020_10_26_351783 537 5 of of IN 10_1101-2020_10_26_351783 537 6 PASCAL PASCAL NNP 10_1101-2020_10_26_351783 537 7 p p NN 10_1101-2020_10_26_351783 537 8 - - HYPH 10_1101-2020_10_26_351783 537 9 values value NNS 10_1101-2020_10_26_351783 537 10 for for IN 10_1101-2020_10_26_351783 537 11 eight eight CD 10_1101-2020_10_26_351783 537 12 single single JJ 10_1101-2020_10_26_351783 537 13 - - HYPH 10_1101-2020_10_26_351783 537 14 method method NN 10_1101-2020_10_26_351783 537 15 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 537 16 modules module NNS 10_1101-2020_10_26_351783 537 17 , , , 10_1101-2020_10_26_351783 537 18 identified identify VBN 10_1101-2020_10_26_351783 537 19 for for IN 10_1101-2020_10_26_351783 537 20 ten ten CD 10_1101-2020_10_26_351783 537 21 MS MS NNP 10_1101-2020_10_26_351783 537 22 - - HYPH 10_1101-2020_10_26_351783 537 23 related relate VBN 10_1101-2020_10_26_351783 537 24 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 537 25 datasets dataset NNS 10_1101-2020_10_26_351783 537 26 . . . 10_1101-2020_10_26_351783 538 1 Module module JJ 10_1101-2020_10_26_351783 538 2 performance performance NN 10_1101-2020_10_26_351783 538 3 P p NN 10_1101-2020_10_26_351783 538 4 - - HYPH 10_1101-2020_10_26_351783 538 5 values value NNS 10_1101-2020_10_26_351783 538 6 are be VBP 10_1101-2020_10_26_351783 538 7 shown show VBN 10_1101-2020_10_26_351783 538 8 in in IN 10_1101-2020_10_26_351783 538 9 a a DT 10_1101-2020_10_26_351783 538 10 white white NN 10_1101-2020_10_26_351783 538 11 to to IN 10_1101-2020_10_26_351783 538 12 blue blue JJ 10_1101-2020_10_26_351783 538 13 scale scale NN 10_1101-2020_10_26_351783 538 14 , , , 10_1101-2020_10_26_351783 538 15 where where WRB 10_1101-2020_10_26_351783 538 16 any any DT 10_1101-2020_10_26_351783 538 17 shade shade NN 10_1101-2020_10_26_351783 538 18 of of IN 10_1101-2020_10_26_351783 538 19 blue blue JJ 10_1101-2020_10_26_351783 538 20 represents represent VBZ 10_1101-2020_10_26_351783 538 21 a a DT 10_1101-2020_10_26_351783 538 22 significant significant JJ 10_1101-2020_10_26_351783 538 23 module module NN 10_1101-2020_10_26_351783 538 24 ( ( -LRB- 10_1101-2020_10_26_351783 538 25 P p NN 10_1101-2020_10_26_351783 538 26 < < XX 10_1101-2020_10_26_351783 538 27 0.05 0.05 XX 10_1101-2020_10_26_351783 538 28 ) ) -RRB- 10_1101-2020_10_26_351783 538 29 , , , 10_1101-2020_10_26_351783 538 30 white white NNP 10_1101-2020_10_26_351783 538 31 represents represent VBZ 10_1101-2020_10_26_351783 538 32 a a DT 10_1101-2020_10_26_351783 538 33 non non JJ 10_1101-2020_10_26_351783 538 34 - - JJ 10_1101-2020_10_26_351783 538 35 significant significant JJ 10_1101-2020_10_26_351783 538 36 module module NN 10_1101-2020_10_26_351783 538 37 , , , 10_1101-2020_10_26_351783 538 38 and and CC 10_1101-2020_10_26_351783 538 39 grey grey NNP 10_1101-2020_10_26_351783 538 40 represents represent VBZ 10_1101-2020_10_26_351783 538 41 a a DT 10_1101-2020_10_26_351783 538 42 module module NN 10_1101-2020_10_26_351783 538 43 of of IN 10_1101-2020_10_26_351783 538 44 size size NN 10_1101-2020_10_26_351783 538 45 zero zero CD 10_1101-2020_10_26_351783 538 46 . . . 10_1101-2020_10_26_351783 539 1 Datasets dataset NNS 10_1101-2020_10_26_351783 539 2 are be VBP 10_1101-2020_10_26_351783 539 3 classified classify VBN 10_1101-2020_10_26_351783 539 4 into into IN 10_1101-2020_10_26_351783 539 5 the the DT 10_1101-2020_10_26_351783 539 6 reported report VBN 10_1101-2020_10_26_351783 539 7 MS MS NNP 10_1101-2020_10_26_351783 539 8 type type NN 10_1101-2020_10_26_351783 539 9 : : : 10_1101-2020_10_26_351783 539 10 MS MS NNP 10_1101-2020_10_26_351783 539 11 ( ( -LRB- 10_1101-2020_10_26_351783 539 12 blue blue NNP 10_1101-2020_10_26_351783 539 13 ) ) -RRB- 10_1101-2020_10_26_351783 539 14 , , , 10_1101-2020_10_26_351783 539 15 RRMS RRMS NNP 10_1101-2020_10_26_351783 539 16 ( ( -LRB- 10_1101-2020_10_26_351783 539 17 red red NNP 10_1101-2020_10_26_351783 539 18 ) ) -RRB- 10_1101-2020_10_26_351783 539 19 , , , 10_1101-2020_10_26_351783 539 20 PPMS PPMS NNP 10_1101-2020_10_26_351783 539 21 ( ( -LRB- 10_1101-2020_10_26_351783 539 22 green green NNP 10_1101-2020_10_26_351783 539 23 ) ) -RRB- 10_1101-2020_10_26_351783 539 24 , , , 10_1101-2020_10_26_351783 539 25 SPMS SPMS NNP 10_1101-2020_10_26_351783 539 26 ( ( -LRB- 10_1101-2020_10_26_351783 539 27 orange orange NNP 10_1101-2020_10_26_351783 539 28 ) ) -RRB- 10_1101-2020_10_26_351783 539 29 , , , 10_1101-2020_10_26_351783 539 30 and and CC 10_1101-2020_10_26_351783 539 31 CIS CIS NNP 10_1101-2020_10_26_351783 539 32 ( ( -LRB- 10_1101-2020_10_26_351783 539 33 yellow yellow NNP 10_1101-2020_10_26_351783 539 34 ) ) -RRB- 10_1101-2020_10_26_351783 539 35 ; ; : 10_1101-2020_10_26_351783 539 36 and and CC 10_1101-2020_10_26_351783 539 37 four four CD 10_1101-2020_10_26_351783 539 38 cell cell NN 10_1101-2020_10_26_351783 539 39 types type NNS 10_1101-2020_10_26_351783 539 40 : : : 10_1101-2020_10_26_351783 539 41 whole whole JJ 10_1101-2020_10_26_351783 539 42 blood blood NN 10_1101-2020_10_26_351783 539 43 ( ( -LRB- 10_1101-2020_10_26_351783 539 44 maroon maroon NNP 10_1101-2020_10_26_351783 539 45 ) ) -RRB- 10_1101-2020_10_26_351783 539 46 , , , 10_1101-2020_10_26_351783 539 47 PBMCs PBMCs NNP 10_1101-2020_10_26_351783 539 48 ( ( -LRB- 10_1101-2020_10_26_351783 539 49 light light JJ 10_1101-2020_10_26_351783 539 50 brown brown NNP 10_1101-2020_10_26_351783 539 51 ) ) -RRB- 10_1101-2020_10_26_351783 539 52 , , , 10_1101-2020_10_26_351783 539 53 white white NNP 10_1101-2020_10_26_351783 539 54 matter matter NNP 10_1101-2020_10_26_351783 539 55 ( ( -LRB- 10_1101-2020_10_26_351783 539 56 light light JJ 10_1101-2020_10_26_351783 539 57 yellow yellow NNP 10_1101-2020_10_26_351783 539 58 ) ) -RRB- 10_1101-2020_10_26_351783 539 59 , , , 10_1101-2020_10_26_351783 539 60 and and CC 10_1101-2020_10_26_351783 539 61 CD4 cd4 NN 10_1101-2020_10_26_351783 539 62 + + SYM 10_1101-2020_10_26_351783 539 63 T t NN 10_1101-2020_10_26_351783 539 64 cells cell NNS 10_1101-2020_10_26_351783 539 65 ( ( -LRB- 10_1101-2020_10_26_351783 539 66 purple purple NNP 10_1101-2020_10_26_351783 539 67 ) ) -RRB- 10_1101-2020_10_26_351783 539 68 . . . 10_1101-2020_10_26_351783 540 1 Datasets dataset NNS 10_1101-2020_10_26_351783 540 2 are be VBP 10_1101-2020_10_26_351783 540 3 meta meta JJ 10_1101-2020_10_26_351783 540 4 P- p- JJ 10_1101-2020_10_26_351783 540 5 values value NNS 10_1101-2020_10_26_351783 540 6 of of IN 10_1101-2020_10_26_351783 540 7 the the DT 10_1101-2020_10_26_351783 540 8 single single JJ 10_1101-2020_10_26_351783 540 9 - - HYPH 10_1101-2020_10_26_351783 540 10 method method NN 10_1101-2020_10_26_351783 540 11 enrichments enrichment NNS 10_1101-2020_10_26_351783 540 12 ( ( -LRB- 10_1101-2020_10_26_351783 540 13 dataset dataset NNP 10_1101-2020_10_26_351783 540 14 score score NN 10_1101-2020_10_26_351783 540 15 , , , 10_1101-2020_10_26_351783 540 16 bottom bottom JJ 10_1101-2020_10_26_351783 540 17 boxplot boxplot NN 10_1101-2020_10_26_351783 540 18 ) ) -RRB- 10_1101-2020_10_26_351783 540 19 . . . 10_1101-2020_10_26_351783 541 1 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 541 2 methods method NNS 10_1101-2020_10_26_351783 541 3 are be VBP 10_1101-2020_10_26_351783 541 4 organized organize VBN 10_1101-2020_10_26_351783 541 5 by by IN 10_1101-2020_10_26_351783 541 6 algorithm algorithm NNP 10_1101-2020_10_26_351783 541 7 type type NN 10_1101-2020_10_26_351783 541 8 : : : 10_1101-2020_10_26_351783 541 9 seed seed NN 10_1101-2020_10_26_351783 541 10 - - HYPH 10_1101-2020_10_26_351783 541 11 based base VBN 10_1101-2020_10_26_351783 541 12 ( ( -LRB- 10_1101-2020_10_26_351783 541 13 green green NNP 10_1101-2020_10_26_351783 541 14 ) ) -RRB- 10_1101-2020_10_26_351783 541 15 , , , 10_1101-2020_10_26_351783 541 16 co co NN 10_1101-2020_10_26_351783 541 17 - - NN 10_1101-2020_10_26_351783 541 18 expression expression NN 10_1101-2020_10_26_351783 541 19 - - HYPH 10_1101-2020_10_26_351783 541 20 based base VBN 10_1101-2020_10_26_351783 541 21 ( ( -LRB- 10_1101-2020_10_26_351783 541 22 yellow yellow NNP 10_1101-2020_10_26_351783 541 23 ) ) -RRB- 10_1101-2020_10_26_351783 541 24 , , , 10_1101-2020_10_26_351783 541 25 and and CC 10_1101-2020_10_26_351783 541 26 clique clique NN 10_1101-2020_10_26_351783 541 27 - - HYPH 10_1101-2020_10_26_351783 541 28 based base VBN 10_1101-2020_10_26_351783 541 29 ( ( -LRB- 10_1101-2020_10_26_351783 541 30 red red NNP 10_1101-2020_10_26_351783 541 31 ) ) -RRB- 10_1101-2020_10_26_351783 541 32 . . . 10_1101-2020_10_26_351783 542 1 Single single JJ 10_1101-2020_10_26_351783 542 2 methods method NNS 10_1101-2020_10_26_351783 542 3 are be VBP 10_1101-2020_10_26_351783 542 4 scored score VBN 10_1101-2020_10_26_351783 542 5 by by IN 10_1101-2020_10_26_351783 542 6 P p NN 10_1101-2020_10_26_351783 542 7 of of IN 10_1101-2020_10_26_351783 542 8 the the DT 10_1101-2020_10_26_351783 542 9 significant significant JJ 10_1101-2020_10_26_351783 542 10 modules module NNS 10_1101-2020_10_26_351783 542 11 across across IN 10_1101-2020_10_26_351783 542 12 datasets dataset NNS 10_1101-2020_10_26_351783 542 13 ( ( -LRB- 10_1101-2020_10_26_351783 542 14 method method NN 10_1101-2020_10_26_351783 542 15 score score NN 10_1101-2020_10_26_351783 542 16 , , , 10_1101-2020_10_26_351783 542 17 right right JJ 10_1101-2020_10_26_351783 542 18 boxplot boxplot NN 10_1101-2020_10_26_351783 542 19 ) ) -RRB- 10_1101-2020_10_26_351783 542 20 . . . 10_1101-2020_10_26_351783 543 1 ( ( -LRB- 10_1101-2020_10_26_351783 543 2 b b NN 10_1101-2020_10_26_351783 543 3 ) ) -RRB- 10_1101-2020_10_26_351783 543 4 Heatmap Heatmap NNP 10_1101-2020_10_26_351783 543 5 of of IN 10_1101-2020_10_26_351783 543 6 PASCAL PASCAL NNP 10_1101-2020_10_26_351783 543 7 p p NN 10_1101-2020_10_26_351783 543 8 - - HYPH 10_1101-2020_10_26_351783 543 9 values value NNS 10_1101-2020_10_26_351783 543 10 for for IN 10_1101-2020_10_26_351783 543 11 four four CD 10_1101-2020_10_26_351783 543 12 single single JJ 10_1101-2020_10_26_351783 543 13 - - HYPH 10_1101-2020_10_26_351783 543 14 method method NN 10_1101-2020_10_26_351783 543 15 MODifieR MODifieR NNP 10_1101-2020_10_26_351783 543 16 modules module NNS 10_1101-2020_10_26_351783 543 17 , , , 10_1101-2020_10_26_351783 543 18 identified identify VBN 10_1101-2020_10_26_351783 543 19 for for IN 10_1101-2020_10_26_351783 543 20 nine nine CD 10_1101-2020_10_26_351783 543 21 MS MS NNP 10_1101-2020_10_26_351783 543 22 - - HYPH 10_1101-2020_10_26_351783 543 23 related relate VBN 10_1101-2020_10_26_351783 543 24 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 543 25 datasets dataset NNS 10_1101-2020_10_26_351783 543 26 . . . 10_1101-2020_10_26_351783 544 1 ( ( -LRB- 10_1101-2020_10_26_351783 544 2 c c NN 10_1101-2020_10_26_351783 544 3 - - HYPH 10_1101-2020_10_26_351783 544 4 d d NNP 10_1101-2020_10_26_351783 544 5 ) ) -RRB- 10_1101-2020_10_26_351783 544 6 Bar bar NN 10_1101-2020_10_26_351783 544 7 plots plot NNS 10_1101-2020_10_26_351783 544 8 of of IN 10_1101-2020_10_26_351783 544 9 Pascal pascal JJ 10_1101-2020_10_26_351783 544 10 p p NN 10_1101-2020_10_26_351783 544 11 - - HYPH 10_1101-2020_10_26_351783 544 12 values value NNS 10_1101-2020_10_26_351783 544 13 for for IN 10_1101-2020_10_26_351783 544 14 the the DT 10_1101-2020_10_26_351783 544 15 MS MS NNP 10_1101-2020_10_26_351783 544 16 consensus consensus NN 10_1101-2020_10_26_351783 544 17 modules module NNS 10_1101-2020_10_26_351783 544 18 generated generate VBN 10_1101-2020_10_26_351783 544 19 with with IN 10_1101-2020_10_26_351783 544 20 Clique Clique NNP 10_1101-2020_10_26_351783 544 21 SuM sum NN 10_1101-2020_10_26_351783 544 22 from from IN 10_1101-2020_10_26_351783 544 23 transcriptomic transcriptomic NNP 10_1101-2020_10_26_351783 544 24 ( ( -LRB- 10_1101-2020_10_26_351783 544 25 a a DT 10_1101-2020_10_26_351783 544 26 ) ) -RRB- 10_1101-2020_10_26_351783 544 27 and and CC 10_1101-2020_10_26_351783 544 28 methylomic methylomic NNP 10_1101-2020_10_26_351783 544 29 ( ( -LRB- 10_1101-2020_10_26_351783 544 30 b b NN 10_1101-2020_10_26_351783 544 31 ) ) -RRB- 10_1101-2020_10_26_351783 544 32 datasets dataset NNS 10_1101-2020_10_26_351783 544 33 . . . 10_1101-2020_10_26_351783 545 1 ( ( -LRB- 10_1101-2020_10_26_351783 545 2 e e LS 10_1101-2020_10_26_351783 545 3 ) ) -RRB- 10_1101-2020_10_26_351783 545 4 Union union NN 10_1101-2020_10_26_351783 545 5 and and CC 10_1101-2020_10_26_351783 545 6 intersection intersection NN 10_1101-2020_10_26_351783 545 7 of of IN 10_1101-2020_10_26_351783 545 8 the the DT 10_1101-2020_10_26_351783 545 9 top top JJ 10_1101-2020_10_26_351783 545 10 performing perform VBG 10_1101-2020_10_26_351783 545 11 modules module NNS 10_1101-2020_10_26_351783 545 12 , , , 10_1101-2020_10_26_351783 545 13 shown show VBN 10_1101-2020_10_26_351783 545 14 as as IN 10_1101-2020_10_26_351783 545 15 a a DT 10_1101-2020_10_26_351783 545 16 Venn Venn NNP 10_1101-2020_10_26_351783 545 17 diagram diagram NN 10_1101-2020_10_26_351783 545 18 . . . 10_1101-2020_10_26_351783 546 1 Diseas Diseas NNP 10_1101-2020_10_26_351783 546 2 e e NNP 10_1101-2020_10_26_351783 546 3 Type Type NNP 10_1101-2020_10_26_351783 546 4 MS MS NNP 10_1101-2020_10_26_351783 546 5 RRMS RRMS NNP 10_1101-2020_10_26_351783 546 6 PPMS PPMS NNP 10_1101-2020_10_26_351783 546 7 SPMS SPMS NNP 10_1101-2020_10_26_351783 546 8 CIS CIS NNP 10_1101-2020_10_26_351783 546 9 Module Module NNP 10_1101-2020_10_26_351783 546 10 Performance Performance NNP 10_1101-2020_10_26_351783 546 11 α α NNP 10_1101-2020_10_26_351783 546 12 = = NNS 10_1101-2020_10_26_351783 546 13 .05 .05 CD 10_1101-2020_10_26_351783 546 14 1 1 CD 10_1101-2020_10_26_351783 546 15 10 10 CD 10_1101-2020_10_26_351783 546 16 - - SYM 10_1101-2020_10_26_351783 546 17 2 2 CD 10_1101-2020_10_26_351783 546 18 10 10 CD 10_1101-2020_10_26_351783 546 19 - - SYM 10_1101-2020_10_26_351783 546 20 3 3 CD 10_1101-2020_10_26_351783 546 21 10 10 CD 10_1101-2020_10_26_351783 546 22 - - SYM 10_1101-2020_10_26_351783 546 23 4 4 CD 10_1101-2020_10_26_351783 546 24 ≤10 ≤10 NNP 10_1101-2020_10_26_351783 546 25 - - HYPH 10_1101-2020_10_26_351783 546 26 5Best 5best NN 10_1101-2020_10_26_351783 546 27 Worst bad JJS 10_1101-2020_10_26_351783 546 28 P p NN 10_1101-2020_10_26_351783 546 29 Cell Cell NNP 10_1101-2020_10_26_351783 546 30 Type Type NNP 10_1101-2020_10_26_351783 546 31 WB WB NNP 10_1101-2020_10_26_351783 546 32 PBMCs PBMCs NNP 10_1101-2020_10_26_351783 546 33 WM WM NNP 10_1101-2020_10_26_351783 546 34 CD4 cd4 NN 10_1101-2020_10_26_351783 546 35 + + SYM 10_1101-2020_10_26_351783 546 36 T t NN 10_1101-2020_10_26_351783 546 37 cells cell NNS 10_1101-2020_10_26_351783 546 38 CD14 CD14 NNP 10_1101-2020_10_26_351783 546 39 + + CC 10_1101-2020_10_26_351783 546 40 Monocytes Monocytes NNP 10_1101-2020_10_26_351783 546 41 CD19 CD19 NNP 10_1101-2020_10_26_351783 546 42 + + CC 10_1101-2020_10_26_351783 546 43 B b NN 10_1101-2020_10_26_351783 546 44 cells cell NNS 10_1101-2020_10_26_351783 546 45 CD8 CD8 NNP 10_1101-2020_10_26_351783 546 46 + + CC 10_1101-2020_10_26_351783 546 47 T t NN 10_1101-2020_10_26_351783 546 48 cells cell NNS 10_1101-2020_10_26_351783 546 49 a a DT 10_1101-2020_10_26_351783 546 50 b b NN 10_1101-2020_10_26_351783 546 51 c c NN 10_1101-2020_10_26_351783 546 52 d d NNP 10_1101-2020_10_26_351783 546 53 e e NNP 10_1101-2020_10_26_351783 546 54 0 0 CD 10_1101-2020_10_26_351783 546 55 2 2 CD 10_1101-2020_10_26_351783 546 56 4 4 CD 10_1101-2020_10_26_351783 546 57 6 6 CD 10_1101-2020_10_26_351783 546 58 8 8 CD 10_1101-2020_10_26_351783 546 59 1/4 1/4 CD 10_1101-2020_10_26_351783 546 60 2/4 2/4 CD 10_1101-2020_10_26_351783 546 61 3/4 3/4 CD 10_1101-2020_10_26_351783 546 62 4/4 4/4 CD 10_1101-2020_10_26_351783 546 63 Transcriptomic Transcriptomic NNP 10_1101-2020_10_26_351783 546 64 Cliq Cliq NNP 10_1101-2020_10_26_351783 546 65 ue ue JJ 10_1101-2020_10_26_351783 546 66 SuM sum NN 10_1101-2020_10_26_351783 546 67 consensus consensus NN 10_1101-2020_10_26_351783 546 68 modules modules NNP 10_1101-2020_10_26_351783 546 69 α α NNP 10_1101-2020_10_26_351783 546 70 -l -l NN 10_1101-2020_10_26_351783 546 71 o o NN 10_1101-2020_10_26_351783 546 72 g g NN 10_1101-2020_10_26_351783 546 73 1 1 CD 10_1101-2020_10_26_351783 546 74 0 0 CD 10_1101-2020_10_26_351783 546 75 P p NN 10_1101-2020_10_26_351783 546 76 * * NFP 10_1101-2020_10_26_351783 546 77 0 0 CD 10_1101-2020_10_26_351783 546 78 2 2 CD 10_1101-2020_10_26_351783 546 79 4 4 CD 10_1101-2020_10_26_351783 546 80 6 6 CD 10_1101-2020_10_26_351783 546 81 8 8 CD 10_1101-2020_10_26_351783 546 82 α α NN 10_1101-2020_10_26_351783 546 83 -l -l NN 10_1101-2020_10_26_351783 546 84 o o NN 10_1101-2020_10_26_351783 546 85 g g NN 10_1101-2020_10_26_351783 546 86 1 1 CD 10_1101-2020_10_26_351783 546 87 0 0 CD 10_1101-2020_10_26_351783 546 88 P p NN 10_1101-2020_10_26_351783 546 89 1/4 1/4 CD 10_1101-2020_10_26_351783 546 90 2/4 2/4 CD 10_1101-2020_10_26_351783 546 91 3/4 3/4 CD 10_1101-2020_10_26_351783 546 92 4/4 4/4 CD 10_1101-2020_10_26_351783 546 93 Methylomic Methylomic NNP 10_1101-2020_10_26_351783 546 94 Cliq Cliq NNP 10_1101-2020_10_26_351783 546 95 ue ue NNP 10_1101-2020_10_26_351783 546 96 SuM SuM NNP 10_1101-2020_10_26_351783 546 97 consensus consensus NN 10_1101-2020_10_26_351783 546 98 modules module VBZ 10_1101-2020_10_26_351783 546 99 * * NFP 10_1101-2020_10_26_351783 546 100 Best good JJS 10_1101-2020_10_26_351783 546 101 transcriptomic transcriptomic JJ 10_1101-2020_10_26_351783 546 102 consensus consensus NN 10_1101-2020_10_26_351783 546 103 Best well RBS 10_1101-2020_10_26_351783 546 104 methylomic methylomic JJ 10_1101-2020_10_26_351783 546 105 consensus consensus NN 10_1101-2020_10_26_351783 546 106 IntersectionUnion IntersectionUnion NNP 10_1101-2020_10_26_351783 546 107 ngenes ngene NNS 10_1101-2020_10_26_351783 546 108 1041332 1041332 CD 10_1101-2020_10_26_351783 546 109 220 220 CD 10_1101-2020_10_26_351783 546 110 1656 1656 CD 10_1101-2020_10_26_351783 546 111 * * NFP 10_1101-2020_10_26_351783 546 112 ( ( -LRB- 10_1101-2020_10_26_351783 546 113 P p NN 10_1101-2020_10_26_351783 546 114 = = SYM 10_1101-2020_10_26_351783 546 115 4.82 4.82 CD 10_1101-2020_10_26_351783 546 116 x x SYM 10_1101-2020_10_26_351783 546 117 10 10 CD 10_1101-2020_10_26_351783 546 118 -8 -8 . 10_1101-2020_10_26_351783 546 119 ) ) -RRB- 10_1101-2020_10_26_351783 546 120 ( ( -LRB- 10_1101-2020_10_26_351783 546 121 P p NN 10_1101-2020_10_26_351783 546 122 = = SYM 10_1101-2020_10_26_351783 546 123 3.74 3.74 CD 10_1101-2020_10_26_351783 546 124 x x SYM 10_1101-2020_10_26_351783 546 125 10 10 CD 10_1101-2020_10_26_351783 546 126 -8 -8 . 10_1101-2020_10_26_351783 546 127 ) ) -RRB- 10_1101-2020_10_26_351783 546 128 ( ( -LRB- 10_1101-2020_10_26_351783 546 129 P p NN 10_1101-2020_10_26_351783 546 130 = = SYM 10_1101-2020_10_26_351783 546 131 1.95 1.95 CD 10_1101-2020_10_26_351783 546 132 x x SYM 10_1101-2020_10_26_351783 546 133 10 10 CD 10_1101-2020_10_26_351783 546 134 -8 -8 . 10_1101-2020_10_26_351783 546 135 ) ) -RRB- 10_1101-2020_10_26_351783 546 136 ( ( -LRB- 10_1101-2020_10_26_351783 546 137 P p NN 10_1101-2020_10_26_351783 546 138 = = SYM 10_1101-2020_10_26_351783 546 139 8.76 8.76 CD 10_1101-2020_10_26_351783 546 140 x x SYM 10_1101-2020_10_26_351783 546 141 10 10 CD 10_1101-2020_10_26_351783 546 142 -9 -9 CD 10_1101-2020_10_26_351783 546 143 ) ) -RRB- 10_1101-2020_10_26_351783 546 144 Diseas Diseas NNP 10_1101-2020_10_26_351783 546 145 e e NNP 10_1101-2020_10_26_351783 546 146 Type Type NNP 10_1101-2020_10_26_351783 546 147 Cell Cell NNP 10_1101-2020_10_26_351783 546 148 Type Type NNP 10_1101-2020_10_26_351783 546 149 Mod Mod NNP 10_1101-2020_10_26_351783 546 150 . . . 10_1101-2020_10_26_351783 547 1 Disco Disco NNP 10_1101-2020_10_26_351783 547 2 v. v. CC 10_1101-2020_10_26_351783 547 3 MCODE MCODE NNP 10_1101-2020_10_26_351783 547 4 Correl Correl NNP 10_1101-2020_10_26_351783 547 5 . . . 10_1101-2020_10_26_351783 548 1 Clique Clique NNP 10_1101-2020_10_26_351783 548 2 Clique Clique NNP 10_1101-2020_10_26_351783 548 3 SuM SuM VBD 10_1101-2020_10_26_351783 548 4 WGCNA wgcna NN 10_1101-2020_10_26_351783 548 5 MODA moda NN 10_1101-2020_10_26_351783 548 6 Di Di NNP 10_1101-2020_10_26_351783 548 7 � � NNP 10_1101-2020_10_26_351783 548 8 � � NNP 10_1101-2020_10_26_351783 548 9 CoEx CoEx NNP 10_1101-2020_10_26_351783 548 10 DIAMOnD diamond NN 10_1101-2020_10_26_351783 548 11 T1 T1 NNP 10_1101-2020_10_26_351783 548 12 2 2 CD 10_1101-2020_10_26_351783 548 13 4 4 CD 10_1101-2020_10_26_351783 548 14 6 6 CD 10_1101-2020_10_26_351783 548 15 8 8 CD 10_1101-2020_10_26_351783 548 16 0 0 CD 10_1101-2020_10_26_351783 548 17 α α NN 10_1101-2020_10_26_351783 548 18 = = NNS 10_1101-2020_10_26_351783 548 19 .05 .05 CD 10_1101-2020_10_26_351783 548 20 0 0 CD 10_1101-2020_10_26_351783 548 21 2 2 CD 10_1101-2020_10_26_351783 548 22 4 4 CD 10_1101-2020_10_26_351783 548 23 6 6 CD 10_1101-2020_10_26_351783 548 24 8 8 CD 10_1101-2020_10_26_351783 548 25 α α NN 10_1101-2020_10_26_351783 548 26 = = NNS 10_1101-2020_10_26_351783 548 27 .05 .05 CD 10_1101-2020_10_26_351783 548 28 11.5 11.5 CD 10_1101-2020_10_26_351783 548 29 -log10P -log10p JJ 10_1101-2020_10_26_351783 548 30 Disease Disease NNP 10_1101-2020_10_26_351783 548 31 Type Type NNP 10_1101-2020_10_26_351783 548 32 Cell Cell NNP 10_1101-2020_10_26_351783 548 33 Type Type NNP 10_1101-2020_10_26_351783 548 34 Mod Mod NNP 10_1101-2020_10_26_351783 548 35 . . . 10_1101-2020_10_26_351783 549 1 Disco Disco NNP 10_1101-2020_10_26_351783 549 2 v. v. CC 10_1101-2020_10_26_351783 549 3 MCODE MCODE NNP 10_1101-2020_10_26_351783 549 4 Correl Correl NNP 10_1101-2020_10_26_351783 549 5 . . . 10_1101-2020_10_26_351783 550 1 Cliq Cliq NNP 10_1101-2020_10_26_351783 550 2 ue ue NNP 10_1101-2020_10_26_351783 550 3 Clique Clique NNP 10_1101-2020_10_26_351783 550 4 SuM SuM VBD 10_1101-2020_10_26_351783 550 5 WGCNA wgcna NN 10_1101-2020_10_26_351783 550 6 MODA moda NN 10_1101-2020_10_26_351783 550 7 Di Di NNP 10_1101-2020_10_26_351783 550 8 � � NNP 10_1101-2020_10_26_351783 550 9 � � NNP 10_1101-2020_10_26_351783 550 10 CoEx CoEx NNP 10_1101-2020_10_26_351783 550 11 DIAMOnD diamond NN 10_1101-2020_10_26_351783 550 12 α α NNP 10_1101-2020_10_26_351783 550 13 = = SYM 10_1101-2020_10_26_351783 550 14 .05 .05 CD 10_1101-2020_10_26_351783 550 15 0 0 CD 10_1101-2020_10_26_351783 550 16 2 2 CD 10_1101-2020_10_26_351783 550 17 4 4 CD 10_1101-2020_10_26_351783 550 18 6 6 CD 10_1101-2020_10_26_351783 550 19 8 8 CD 10_1101-2020_10_26_351783 550 20 -log10P -log10p NN 10_1101-2020_10_26_351783 550 21 T2 t2 NN 10_1101-2020_10_26_351783 550 22 T3 T3 NNP 10_1101-2020_10_26_351783 550 23 T4 T4 NNP 10_1101-2020_10_26_351783 550 24 T5 T5 NNP 10_1101-2020_10_26_351783 550 25 T6 T6 NNP 10_1101-2020_10_26_351783 550 26 T7 t7 NN 10_1101-2020_10_26_351783 550 27 T8 t8 NN 10_1101-2020_10_26_351783 550 28 T9 T9 , 10_1101-2020_10_26_351783 550 29 T10 T10 NNP 10_1101-2020_10_26_351783 550 30 T11 T11 NNP 10_1101-2020_10_26_351783 550 31 M1 M1 NNP 10_1101-2020_10_26_351783 550 32 M2 M2 NNP 10_1101-2020_10_26_351783 550 33 M3 M3 NNP 10_1101-2020_10_26_351783 550 34 M4 M4 NNP 10_1101-2020_10_26_351783 550 35 M5 M5 NNP 10_1101-2020_10_26_351783 550 36 M6 M6 NNP 10_1101-2020_10_26_351783 550 37 M7 M7 NNP 10_1101-2020_10_26_351783 550 38 M8 M8 NNP 10_1101-2020_10_26_351783 550 39 M9 M9 NNP 10_1101-2020_10_26_351783 550 40 NA NA NNP 10_1101-2020_10_26_351783 550 41 NA NA NNP 10_1101-2020_10_26_351783 550 42 NA NA NNP 10_1101-2020_10_26_351783 550 43 NANANA nanana NN 10_1101-2020_10_26_351783 550 44 NA na NN 10_1101-2020_10_26_351783 550 45 NA na IN 10_1101-2020_10_26_351783 550 46 NA NA NNP 10_1101-2020_10_26_351783 550 47 NA NA NNP 10_1101-2020_10_26_351783 550 48 NA NA NNP 10_1101-2020_10_26_351783 550 49 NA NA NNP 10_1101-2020_10_26_351783 550 50 NA NA NNP 10_1101-2020_10_26_351783 550 51 NA NA NNP 10_1101-2020_10_26_351783 550 52 NA NA NNP 10_1101-2020_10_26_351783 550 53 NA NA NNP 10_1101-2020_10_26_351783 550 54 α α NN 10_1101-2020_10_26_351783 550 55 = = NNS 10_1101-2020_10_26_351783 550 56 .05 .05 NFP 10_1101-2020_10_26_351783 550 57 0 0 CD 10_1101-2020_10_26_351783 550 58 2 2 CD 10_1101-2020_10_26_351783 550 59 4 4 CD 10_1101-2020_10_26_351783 550 60 6 6 CD 10_1101-2020_10_26_351783 550 61 8 8 CD 10_1101-2020_10_26_351783 550 62 -l -l NFP 10_1101-2020_10_26_351783 550 63 o o NN 10_1101-2020_10_26_351783 550 64 g g NN 10_1101-2020_10_26_351783 550 65 1 1 CD 10_1101-2020_10_26_351783 550 66 0 0 CD 10_1101-2020_10_26_351783 550 67 P P NNP 10_1101-2020_10_26_351783 550 68 -l -l : 10_1101-2020_10_26_351783 550 69 og og NNP 10_1101-2020_10_26_351783 550 70 1 1 CD 10_1101-2020_10_26_351783 550 71 0 0 CD 10_1101-2020_10_26_351783 550 72 P p NN 10_1101-2020_10_26_351783 550 73 ( ( -LRB- 10_1101-2020_10_26_351783 550 74 which which WDT 10_1101-2020_10_26_351783 550 75 was be VBD 10_1101-2020_10_26_351783 550 76 not not RB 10_1101-2020_10_26_351783 550 77 certified certify VBN 10_1101-2020_10_26_351783 550 78 by by IN 10_1101-2020_10_26_351783 550 79 peer peer NN 10_1101-2020_10_26_351783 550 80 review review NN 10_1101-2020_10_26_351783 550 81 ) ) -RRB- 10_1101-2020_10_26_351783 550 82 is be VBZ 10_1101-2020_10_26_351783 550 83 the the DT 10_1101-2020_10_26_351783 550 84 author author NN 10_1101-2020_10_26_351783 550 85 / / SYM 10_1101-2020_10_26_351783 550 86 funder funder NN 10_1101-2020_10_26_351783 550 87 . . . 10_1101-2020_10_26_351783 551 1 All all DT 10_1101-2020_10_26_351783 551 2 rights right NNS 10_1101-2020_10_26_351783 551 3 reserved reserve VBD 10_1101-2020_10_26_351783 551 4 . . . 10_1101-2020_10_26_351783 552 1 No no DT 10_1101-2020_10_26_351783 552 2 reuse reuse NN 10_1101-2020_10_26_351783 552 3 allowed allow VBN 10_1101-2020_10_26_351783 552 4 without without IN 10_1101-2020_10_26_351783 552 5 permission permission NN 10_1101-2020_10_26_351783 552 6 . . . 10_1101-2020_10_26_351783 553 1 The the DT 10_1101-2020_10_26_351783 553 2 copyright copyright NN 10_1101-2020_10_26_351783 553 3 holder holder NN 10_1101-2020_10_26_351783 553 4 for for IN 10_1101-2020_10_26_351783 553 5 this this DT 10_1101-2020_10_26_351783 553 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 553 7 version version NN 10_1101-2020_10_26_351783 553 8 posted post VBD 10_1101-2020_10_26_351783 553 9 January January NNP 10_1101-2020_10_26_351783 553 10 6 6 CD 10_1101-2020_10_26_351783 553 11 , , , 10_1101-2020_10_26_351783 553 12 2021 2021 CD 10_1101-2020_10_26_351783 553 13 . . . 10_1101-2020_10_26_351783 553 14 ; ; : 10_1101-2020_10_26_351783 553 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 553 16 : : : 10_1101-2020_10_26_351783 553 17 bioRxiv biorxiv IN 10_1101-2020_10_26_351783 553 18 preprint preprint NN 10_1101-2020_10_26_351783 553 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 NNP 10_1101-2020_10_26_351783 553 20 32 32 CD 10_1101-2020_10_26_351783 553 21 Figure figure NN 10_1101-2020_10_26_351783 553 22 5 5 CD 10_1101-2020_10_26_351783 553 23 . . . 10_1101-2020_10_26_351783 554 1 Risk risk NN 10_1101-2020_10_26_351783 554 2 factor factor NN 10_1101-2020_10_26_351783 554 3 enrichment enrichment NN 10_1101-2020_10_26_351783 554 4 and and CC 10_1101-2020_10_26_351783 554 5 network network NN 10_1101-2020_10_26_351783 554 6 visualization visualization NN 10_1101-2020_10_26_351783 554 7 of of IN 10_1101-2020_10_26_351783 554 8 the the DT 10_1101-2020_10_26_351783 554 9 MS MS NNP 10_1101-2020_10_26_351783 554 10 multi multi JJ 10_1101-2020_10_26_351783 554 11 - - JJ 10_1101-2020_10_26_351783 554 12 omic omic JJ 10_1101-2020_10_26_351783 554 13 module module NN 10_1101-2020_10_26_351783 554 14 . . . 10_1101-2020_10_26_351783 555 1 ( ( -LRB- 10_1101-2020_10_26_351783 555 2 a a LS 10_1101-2020_10_26_351783 555 3 ) ) -RRB- 10_1101-2020_10_26_351783 555 4 Evidence evidence NN 10_1101-2020_10_26_351783 555 5 levels level NNS 10_1101-2020_10_26_351783 555 6 and and CC 10_1101-2020_10_26_351783 555 7 effect effect NN 10_1101-2020_10_26_351783 555 8 on on IN 10_1101-2020_10_26_351783 555 9 MS MS NNP 10_1101-2020_10_26_351783 555 10 of of IN 10_1101-2020_10_26_351783 555 11 the the DT 10_1101-2020_10_26_351783 555 12 risk risk NN 10_1101-2020_10_26_351783 555 13 factor factor NN 10_1101-2020_10_26_351783 555 14 . . . 10_1101-2020_10_26_351783 556 1 � � NNP 10_1101-2020_10_26_351783 556 2 ( ( -LRB- 10_1101-2020_10_26_351783 556 3 b b LS 10_1101-2020_10_26_351783 556 4 ) ) -RRB- 10_1101-2020_10_26_351783 556 5 Enrichment Enrichment NNP 10_1101-2020_10_26_351783 556 6 overlap overlap NN 10_1101-2020_10_26_351783 556 7 of of IN 10_1101-2020_10_26_351783 556 8 multi multi JJ 10_1101-2020_10_26_351783 556 9 - - JJ 10_1101-2020_10_26_351783 556 10 omic omic JJ 10_1101-2020_10_26_351783 556 11 MS MS NNP 10_1101-2020_10_26_351783 556 12 DYNC1H1 DYNC1H1 NNP 10_1101-2020_10_26_351783 556 13 JUN JUN NNP 10_1101-2020_10_26_351783 556 14 MAPK9 MAPK9 . 10_1101-2020_10_26_351783 556 15 MAPK8 MAPK8 NNP 10_1101-2020_10_26_351783 556 16 PRKCA PRKCA NNP 10_1101-2020_10_26_351783 556 17 PRKCE prkce NN 10_1101-2020_10_26_351783 556 18 MAPK11 MAPK11 NNS 10_1101-2020_10_26_351783 556 19 LCP2 lcp2 NN 10_1101-2020_10_26_351783 556 20 RHOA rhoa NN 10_1101-2020_10_26_351783 556 21 DYNLL1 dynll1 VBP 10_1101-2020_10_26_351783 556 22 GRAP2 GRAP2 '' 10_1101-2020_10_26_351783 556 23 BCL6 BCL6 NNP 10_1101-2020_10_26_351783 556 24 DNM3 DNM3 NNP 10_1101-2020_10_26_351783 556 25 DNM1 DNM1 NNP 10_1101-2020_10_26_351783 556 26 PRKACB PRKACB NNP 10_1101-2020_10_26_351783 556 27 CASP3 CASP3 NNP 10_1101-2020_10_26_351783 556 28 BCL2 BCL2 NNP 10_1101-2020_10_26_351783 556 29 NRIP1 nrip1 NN 10_1101-2020_10_26_351783 556 30 DNM2 DNM2 NNP 10_1101-2020_10_26_351783 556 31 BCL2L11 bcl2l11 VB 10_1101-2020_10_26_351783 556 32 PRKACA PRKACA NNP 10_1101-2020_10_26_351783 556 33 PTEN PTEN NNP 10_1101-2020_10_26_351783 556 34 ATF2 ATF2 NNP 10_1101-2020_10_26_351783 556 35 PRKCI PRKCI NNP 10_1101-2020_10_26_351783 556 36 BID BID NNP 10_1101-2020_10_26_351783 556 37 RAC1 RAC1 NNP 10_1101-2020_10_26_351783 556 38 RAC2 RAC2 NNP 10_1101-2020_10_26_351783 556 39 RASA1 RASA1 VBZ 10_1101-2020_10_26_351783 556 40 NRAS NRAS NNP 10_1101-2020_10_26_351783 556 41 SOS1 SOS1 NNP 10_1101-2020_10_26_351783 556 42 PIK3CA pik3ca JJ 10_1101-2020_10_26_351783 556 43 HRAS HRAS NNP 10_1101-2020_10_26_351783 556 44 CASP8 CASP8 . 10_1101-2020_10_26_351783 556 45 CDC42 cdc42 CD 10_1101-2020_10_26_351783 556 46 PRKCZ PRKCZ VBN 10_1101-2020_10_26_351783 556 47 PARD6A PARD6A NNP 10_1101-2020_10_26_351783 556 48 MET MET NNP 10_1101-2020_10_26_351783 556 49 PLCG1 PLCG1 NNS 10_1101-2020_10_26_351783 556 50 IRS1 IRS1 NNP 10_1101-2020_10_26_351783 556 51 PTK2 PTK2 NNP 10_1101-2020_10_26_351783 556 52 PGR PGR NNP 10_1101-2020_10_26_351783 556 53 KRAS KRAS NNP 10_1101-2020_10_26_351783 556 54 RET RET NNP 10_1101-2020_10_26_351783 556 55 HGF HGF NNP 10_1101-2020_10_26_351783 556 56 PIK3CB pik3cb NN 10_1101-2020_10_26_351783 556 57 GAB1 GAB1 NNP 10_1101-2020_10_26_351783 556 58 VAV1 VAV1 NNP 10_1101-2020_10_26_351783 556 59 GRB2 GRB2 NNP 10_1101-2020_10_26_351783 556 60 ERBB2 ERBB2 NNP 10_1101-2020_10_26_351783 556 61 HCK HCK NNP 10_1101-2020_10_26_351783 556 62 PIK3CD pik3cd NN 10_1101-2020_10_26_351783 556 63 CRKL CRKL NNS 10_1101-2020_10_26_351783 556 64 PIK3R2 pik3r2 RB 10_1101-2020_10_26_351783 556 65 CARM1 CARM1 : 10_1101-2020_10_26_351783 556 66 IGF1 IGF1 NNP 10_1101-2020_10_26_351783 556 67 PTK2B ptk2b CD 10_1101-2020_10_26_351783 556 68 KDR KDR NNP 10_1101-2020_10_26_351783 556 69 VEGFA VEGFA NNP 10_1101-2020_10_26_351783 556 70 PXN PXN NNP 10_1101-2020_10_26_351783 556 71 EDN1 EDN1 NNPS 10_1101-2020_10_26_351783 556 72 CBL CBL NNP 10_1101-2020_10_26_351783 556 73 BCAR1 bcar1 VBP 10_1101-2020_10_26_351783 556 74 APP APP NNP 10_1101-2020_10_26_351783 556 75 SH3GL2 SH3GL2 NNP 10_1101-2020_10_26_351783 556 76 IQGAP1 IQGAP1 '' 10_1101-2020_10_26_351783 556 77 SHC1 SHC1 NNP 10_1101-2020_10_26_351783 556 78 BDNF BDNF NNP 10_1101-2020_10_26_351783 556 79 NGF NGF NNP 10_1101-2020_10_26_351783 556 80 NTRK1 NTRK1 NNP 10_1101-2020_10_26_351783 556 81 PTPN6 PTPN6 NNP 10_1101-2020_10_26_351783 556 82 EGFR EGFR NNP 10_1101-2020_10_26_351783 556 83 INS INS NNP 10_1101-2020_10_26_351783 556 84 GNB1 GNB1 NNP 10_1101-2020_10_26_351783 556 85 GNG2 GNG2 NNP 10_1101-2020_10_26_351783 556 86 ARID1A arid1a CD 10_1101-2020_10_26_351783 556 87 TRIM25 trim25 NN 10_1101-2020_10_26_351783 556 88 GNAI1 GNAI1 NNS 10_1101-2020_10_26_351783 556 89 AR AR NNP 10_1101-2020_10_26_351783 556 90 PIK3R3 PIK3R3 : 10_1101-2020_10_26_351783 556 91 PIK3R1 pik3r1 ADD 10_1101-2020_10_26_351783 556 92 PTPRJ PTPRJ NNP 10_1101-2020_10_26_351783 556 93 SP1 SP1 NNP 10_1101-2020_10_26_351783 556 94 INPP5B INPP5B NNP 10_1101-2020_10_26_351783 556 95 TNF TNF NNP 10_1101-2020_10_26_351783 556 96 CTNNB1 CTNNB1 VBZ 10_1101-2020_10_26_351783 556 97 NCAM1 NCAM1 NNP 10_1101-2020_10_26_351783 556 98 CDH1 CDH1 NNP 10_1101-2020_10_26_351783 556 99 SPP1 SPP1 NNPS 10_1101-2020_10_26_351783 556 100 SEC13 SEC13 NNP 10_1101-2020_10_26_351783 556 101 CSK CSK NNP 10_1101-2020_10_26_351783 556 102 TLN1 TLN1 NNP 10_1101-2020_10_26_351783 556 103 RAP1B RAP1B -LRB- 10_1101-2020_10_26_351783 556 104 ABL ABL NNP 10_1101-2020_10_26_351783 556 105 1SRC 1src NN 10_1101-2020_10_26_351783 556 106 ITGB3 itgb3 NN 10_1101-2020_10_26_351783 556 107 PTPN11 ptpn11 UH 10_1101-2020_10_26_351783 556 108 EGF EGF NNP 10_1101-2020_10_26_351783 556 109 IT IT NNP 10_1101-2020_10_26_351783 556 110 GB1 GB1 NNP 10_1101-2020_10_26_351783 556 111 ITGAV ITGAV NNP 10_1101-2020_10_26_351783 556 112 SYNJ2 synj2 JJ 10_1101-2020_10_26_351783 556 113 CD7 CD7 NNP 10_1101-2020_10_26_351783 556 114 4 4 CD 10_1101-2020_10_26_351783 556 115 HLA HLA NNP 10_1101-2020_10_26_351783 556 116 - - HYPH 10_1101-2020_10_26_351783 556 117 E e NN 10_1101-2020_10_26_351783 556 118 CLTA CLTA NNP 10_1101-2020_10_26_351783 556 119 CD4 CD4 NNP 10_1101-2020_10_26_351783 556 120 HLA HLA NNP 10_1101-2020_10_26_351783 556 121 - - HYPH 10_1101-2020_10_26_351783 556 122 DPB1 DPB1 NNP 10_1101-2020_10_26_351783 556 123 HLA HLA NNP 10_1101-2020_10_26_351783 556 124 - - , 10_1101-2020_10_26_351783 556 125 A a NN 10_1101-2020_10_26_351783 556 126 PTPN22 PTPN22 NNP 10_1101-2020_10_26_351783 556 127 HLA HLA NNP 10_1101-2020_10_26_351783 556 128 - - HYPH 10_1101-2020_10_26_351783 556 129 DRA DRA NNP 10_1101-2020_10_26_351783 556 130 IL IL NNP 10_1101-2020_10_26_351783 556 131 10 10 CD 10_1101-2020_10_26_351783 556 132 MMP9 MMP9 NNP 10_1101-2020_10_26_351783 556 133 PIP5K1B pip5k1b RB 10_1101-2020_10_26_351783 556 134 CXCR4 cxcr4 JJ 10_1101-2020_10_26_351783 556 135 CXCL12 cxcl12 NN 10_1101-2020_10_26_351783 556 136 ICAM1 ICAM1 '' 10_1101-2020_10_26_351783 556 137 LCKHLA LCKHLA NNP 10_1101-2020_10_26_351783 556 138 - - HYPH 10_1101-2020_10_26_351783 556 139 DRB1 DRB1 NNP 10_1101-2020_10_26_351783 556 140 AP2M1 AP2M1 NNP 10_1101-2020_10_26_351783 556 141 AP2B1 AP2B1 NNP 10_1101-2020_10_26_351783 556 142 FCGR1A FCGR1A NNP 10_1101-2020_10_26_351783 556 143 AP1M1 AP1M1 NNP 10_1101-2020_10_26_351783 556 144 MAPK14 MAPK14 NNP 10_1101-2020_10_26_351783 556 145 VWF VWF NNP 10_1101-2020_10_26_351783 556 146 IRF7 IRF7 NNP 10_1101-2020_10_26_351783 556 147 IRF1 IRF1 NNP 10_1101-2020_10_26_351783 556 148 IRF4 IRF4 NNP 10_1101-2020_10_26_351783 556 149 IL4 IL4 NNP 10_1101-2020_10_26_351783 556 150 IL IL NNP 10_1101-2020_10_26_351783 556 151 6 6 CD 10_1101-2020_10_26_351783 556 152 IFNG IFNG NNP 10_1101-2020_10_26_351783 556 153 AKT3 AKT3 NNP 10_1101-2020_10_26_351783 556 154 A A NNP 10_1101-2020_10_26_351783 556 155 P2 p2 NN 10_1101-2020_10_26_351783 556 156 A2 A2 NNP 10_1101-2020_10_26_351783 556 157 HSP90AA1 HSP90AA1 NNP 10_1101-2020_10_26_351783 556 158 CD3D cd3d JJ 10_1101-2020_10_26_351783 556 159 PPP2R1A PPP2R1A NNP 10_1101-2020_10_26_351783 556 160 GSK3B gsk3b CD 10_1101-2020_10_26_351783 556 161 PPP2CA ppp2ca NN 10_1101-2020_10_26_351783 556 162 FGG FGG NNP 10_1101-2020_10_26_351783 556 163 EPS15L1 EPS15L1 VBZ 10_1101-2020_10_26_351783 556 164 FGF2 FGF2 NNP 10_1101-2020_10_26_351783 556 165 PTPRC PTPRC NNP 10_1101-2020_10_26_351783 556 166 CD3 cd3 NN 10_1101-2020_10_26_351783 556 167 G g NN 10_1101-2020_10_26_351783 556 168 HSP90AB1 hsp90ab1 ADD 10_1101-2020_10_26_351783 556 169 EPHA2 EPHA2 NNP 10_1101-2020_10_26_351783 556 170 F F NNP 10_1101-2020_10_26_351783 556 171 N1 N1 NNP 10_1101-2020_10_26_351783 556 172 CLTC CLTC NNP 10_1101-2020_10_26_351783 556 173 PIP5K1A PIP5K1A NNP 10_1101-2020_10_26_351783 556 174 VCAM1 vcam1 VB 10_1101-2020_10_26_351783 556 175 FYN FYN NNP 10_1101-2020_10_26_351783 556 176 ESR1 ESR1 NNP 10_1101-2020_10_26_351783 556 177 TGFB1 tgfb1 NN 10_1101-2020_10_26_351783 556 178 ITGB2 ITGB2 NNP 10_1101-2020_10_26_351783 556 179 CD8 CD8 NNP 10_1101-2020_10_26_351783 556 180 6 6 CD 10_1101-2020_10_26_351783 556 181 NR3C1 NR3C1 NNP 10_1101-2020_10_26_351783 556 182 CD80 CD80 NNP 10_1101-2020_10_26_351783 556 183 CD3E CD3E NNP 10_1101-2020_10_26_351783 556 184 AP2A1 AP2A1 NNP 10_1101-2020_10_26_351783 556 185 RUNX1 runx1 VBP 10_1101-2020_10_26_351783 556 186 CD28 CD28 NNP 10_1101-2020_10_26_351783 556 187 CD4 CD4 NNP 10_1101-2020_10_26_351783 556 188 4 4 CD 10_1101-2020_10_26_351783 556 189 CEBPB cebpb NN 10_1101-2020_10_26_351783 556 190 AP2S1 ap2s1 NN 10_1101-2020_10_26_351783 556 191 NFKB1 nfkb1 NN 10_1101-2020_10_26_351783 556 192 HDAC1 hdac1 UH 10_1101-2020_10_26_351783 556 193 KIT KIT NNP 10_1101-2020_10_26_351783 556 194 CDK4 CDK4 NNP 10_1101-2020_10_26_351783 556 195 CCNA1 ccna1 POS 10_1101-2020_10_26_351783 556 196 UBE2I ube2i CD 10_1101-2020_10_26_351783 556 197 PCNA PCNA NNP 10_1101-2020_10_26_351783 556 198 CCND1 ccnd1 NN 10_1101-2020_10_26_351783 556 199 RELA rela NN 10_1101-2020_10_26_351783 556 200 STAT5A stat5a NN 10_1101-2020_10_26_351783 556 201 PRKCD PRKCD NNS 10_1101-2020_10_26_351783 556 202 PRKCQ PRKCQ NNP 10_1101-2020_10_26_351783 556 203 ZAP70 zap70 NN 10_1101-2020_10_26_351783 556 204 RAF1 raf1 CD 10_1101-2020_10_26_351783 556 205 YWHAB YWHAB NNP 10_1101-2020_10_26_351783 556 206 AKT1 AKT1 NNP 10_1101-2020_10_26_351783 556 207 CD24 CD24 NNP 10_1101-2020_10_26_351783 556 208 7 7 CD 10_1101-2020_10_26_351783 556 209 RAP1A rap1a CD 10_1101-2020_10_26_351783 556 210 MAPK1 MAPK1 NNS 10_1101-2020_10_26_351783 556 211 MAPK3 mapk3 NN 10_1101-2020_10_26_351783 556 212 PTAFR PTAFR NNP 10_1101-2020_10_26_351783 556 213 RAB7A rab7a PRP 10_1101-2020_10_26_351783 556 214 MAP2K1 map2k1 CD 10_1101-2020_10_26_351783 556 215 SMAD4 smad4 UH 10_1101-2020_10_26_351783 556 216 MAP3K5 MAP3K5 : 10_1101-2020_10_26_351783 556 217 CREBBP crebbp NN 10_1101-2020_10_26_351783 556 218 SMAD2 smad2 NN 10_1101-2020_10_26_351783 556 219 HMGB1 hmgb1 NN 10_1101-2020_10_26_351783 556 220 NGFR NGFR NNP 10_1101-2020_10_26_351783 556 221 DAXX DAXX NNP 10_1101-2020_10_26_351783 556 222 AKT2 AKT2 NNP 10_1101-2020_10_26_351783 556 223 PPARG PPARG NNP 10_1101-2020_10_26_351783 556 224 TRIM2 trim2 VBP 10_1101-2020_10_26_351783 556 225 4 4 CD 10_1101-2020_10_26_351783 556 226 SMAD3 smad3 CD 10_1101-2020_10_26_351783 556 227 MYC MYC NNP 10_1101-2020_10_26_351783 556 228 CTSS CTSS NNP 10_1101-2020_10_26_351783 556 229 SIRT1 SIRT1 NNS 10_1101-2020_10_26_351783 556 230 CSF2 CSF2 NNP 10_1101-2020_10_26_351783 556 231 BRCA1 BRCA1 NNP 10_1101-2020_10_26_351783 556 232 SPTBN2 SPTBN2 . 10_1101-2020_10_26_351783 556 233 TP53 tp53 IN 10_1101-2020_10_26_351783 556 234 H2 H2 NNP 10_1101-2020_10_26_351783 556 235 AX AX NNP 10_1101-2020_10_26_351783 556 236 SPHK1 SPHK1 NNP 10_1101-2020_10_26_351783 556 237 EP3 EP3 NNP 10_1101-2020_10_26_351783 556 238 00 00 CD 10_1101-2020_10_26_351783 556 239 JAK1 JAK1 NNP 10_1101-2020_10_26_351783 556 240 IRF3 IRF3 NNP 10_1101-2020_10_26_351783 556 241 STAT3 STAT3 : 10_1101-2020_10_26_351783 556 242 STAT1 stat1 NN 10_1101-2020_10_26_351783 556 243 STAT6 STAT6 '' 10_1101-2020_10_26_351783 556 244 PAK1 PAK1 NNP 10_1101-2020_10_26_351783 556 245 HIF1A HIF1A NNP 10_1101-2020_10_26_351783 556 246 PLCG2PDGFB PLCG2PDGFB : 10_1101-2020_10_26_351783 556 247 JAK2 JAK2 NNP 10_1101-2020_10_26_351783 556 248 PDGFRB PDGFRB NNP 10_1101-2020_10_26_351783 556 249 CCNE1 ccne1 NN 10_1101-2020_10_26_351783 556 250 RUNX3 RUNX3 VBZ 10_1101-2020_10_26_351783 556 251 RB1 RB1 NNP 10_1101-2020_10_26_351783 556 252 EZH2CDK2 EZH2CDK2 NNP 10_1101-2020_10_26_351783 556 253 Functional functional JJ 10_1101-2020_10_26_351783 556 254 Clusters Clusters NNPS 10_1101-2020_10_26_351783 556 255 Cell Cell NNP 10_1101-2020_10_26_351783 556 256 death death NN 10_1101-2020_10_26_351783 556 257 and and CC 10_1101-2020_10_26_351783 556 258 apoptosis apoptosis NN 10_1101-2020_10_26_351783 556 259 Morphogenesis Morphogenesis NNP 10_1101-2020_10_26_351783 556 260 and and CC 10_1101-2020_10_26_351783 556 261 neurogenesis neurogenesis NN 10_1101-2020_10_26_351783 556 262 Cell Cell NNP 10_1101-2020_10_26_351783 556 263 cycle cycle NN 10_1101-2020_10_26_351783 556 264 and and CC 10_1101-2020_10_26_351783 556 265 proliferation proliferation NN 10_1101-2020_10_26_351783 556 266 Chemotaxis chemotaxi NNS 10_1101-2020_10_26_351783 556 267 and and CC 10_1101-2020_10_26_351783 556 268 cell cell NN 10_1101-2020_10_26_351783 556 269 migration migration NN 10_1101-2020_10_26_351783 556 270 Response Response NNP 10_1101-2020_10_26_351783 556 271 to to IN 10_1101-2020_10_26_351783 556 272 hormone hormone NN 10_1101-2020_10_26_351783 556 273 stimulus stimulus NN 10_1101-2020_10_26_351783 556 274 Leukocyte Leukocyte NNP 10_1101-2020_10_26_351783 556 275 activation activation NN 10_1101-2020_10_26_351783 556 276 and and CC 10_1101-2020_10_26_351783 556 277 di di FW 10_1101-2020_10_26_351783 556 278 � � NNS 10_1101-2020_10_26_351783 556 279 � � , 10_1101-2020_10_26_351783 556 280 erentiation erentiation NN 10_1101-2020_10_26_351783 556 281 Node Node NNP 10_1101-2020_10_26_351783 556 282 Color Color NNP 10_1101-2020_10_26_351783 556 283 Legend Legend NNP 10_1101-2020_10_26_351783 556 284 Low Low NNP 10_1101-2020_10_26_351783 556 285 sun sun NN 10_1101-2020_10_26_351783 556 286 exposure exposure NN 10_1101-2020_10_26_351783 556 287 Smoking Smoking NNP 10_1101-2020_10_26_351783 556 288 High High NNP 10_1101-2020_10_26_351783 556 289 BMI BMI NNP 10_1101-2020_10_26_351783 556 290 Alcohol Alcohol NNP 10_1101-2020_10_26_351783 556 291 use use NN 10_1101-2020_10_26_351783 556 292 EBV EBV NNP 10_1101-2020_10_26_351783 556 293 infection infection NN 10_1101-2020_10_26_351783 556 294 Associated Associated NNP 10_1101-2020_10_26_351783 556 295 with with IN 10_1101-2020_10_26_351783 556 296 MS MS NNP 10_1101-2020_10_26_351783 556 297 Signif Signif NNP 10_1101-2020_10_26_351783 556 298 . . . 10_1101-2020_10_26_351783 557 1 enriched enriched JJ 10_1101-2020_10_26_351783 557 2 MS MS NNP 10_1101-2020_10_26_351783 557 3 risk risk NN 10_1101-2020_10_26_351783 557 4 factors factor NNS 10_1101-2020_10_26_351783 557 5 Risk Risk NNP 10_1101-2020_10_26_351783 557 6 factor factor NN 10_1101-2020_10_26_351783 557 7 Evidence evidence NN 10_1101-2020_10_26_351783 557 8 E e NN 10_1101-2020_10_26_351783 557 9 � � NNP 10_1101-2020_10_26_351783 557 10 � � ADD 10_1101-2020_10_26_351783 557 11 ect ect VBP 10_1101-2020_10_26_351783 557 12 EBV EBV NNP 10_1101-2020_10_26_351783 557 13 infection infection NN 10_1101-2020_10_26_351783 557 14 Smoking Smoking NNP 10_1101-2020_10_26_351783 557 15 Low Low NNP 10_1101-2020_10_26_351783 557 16 sun sun NN 10_1101-2020_10_26_351783 557 17 exposure exposure NN 10_1101-2020_10_26_351783 557 18 Adolescent adolescent JJ 10_1101-2020_10_26_351783 557 19 obesity obesity NN 10_1101-2020_10_26_351783 557 20 High high JJ 10_1101-2020_10_26_351783 557 21 BMI BMI NNP 10_1101-2020_10_26_351783 557 22 Night Night NNP 10_1101-2020_10_26_351783 557 23 shift shift NN 10_1101-2020_10_26_351783 557 24 work work NN 10_1101-2020_10_26_351783 557 25 Organic organic JJ 10_1101-2020_10_26_351783 557 26 solvent solvent NN 10_1101-2020_10_26_351783 557 27 exposure exposure NN 10_1101-2020_10_26_351783 557 28 Alcohol Alcohol NNP 10_1101-2020_10_26_351783 557 29 consumption consumption NN 10_1101-2020_10_26_351783 557 30 Oral oral JJ 10_1101-2020_10_26_351783 557 31 tobacco tobacco NN 10_1101-2020_10_26_351783 557 32 + + CD 10_1101-2020_10_26_351783 557 33 + + SYM 10_1101-2020_10_26_351783 557 34 + + SYM 10_1101-2020_10_26_351783 557 35 + + SYM 10_1101-2020_10_26_351783 557 36 + + SYM 10_1101-2020_10_26_351783 557 37 + + SYM 10_1101-2020_10_26_351783 557 38 + + SYM 10_1101-2020_10_26_351783 557 39 + + SYM 10_1101-2020_10_26_351783 557 40 + + SYM 10_1101-2020_10_26_351783 557 41 + + SYM 10_1101-2020_10_26_351783 557 42 + + SYM 10_1101-2020_10_26_351783 557 43 + + SYM 10_1101-2020_10_26_351783 557 44 + + SYM 10_1101-2020_10_26_351783 557 45 + + SYM 10_1101-2020_10_26_351783 557 46 + + SYM 10_1101-2020_10_26_351783 557 47 + + SYM 10_1101-2020_10_26_351783 557 48 + + SYM 10_1101-2020_10_26_351783 557 49 � � NN 10_1101-2020_10_26_351783 557 50 Risk risk NN 10_1101-2020_10_26_351783 557 51 � � NNP 10_1101-2020_10_26_351783 557 52 Risk Risk NNP 10_1101-2020_10_26_351783 557 53 � � NNP 10_1101-2020_10_26_351783 557 54 Risk Risk NNP 10_1101-2020_10_26_351783 557 55 � � NNP 10_1101-2020_10_26_351783 557 56 Risk Risk NNP 10_1101-2020_10_26_351783 557 57 � � NNP 10_1101-2020_10_26_351783 557 58 Risk Risk NNP 10_1101-2020_10_26_351783 557 59 � � NNP 10_1101-2020_10_26_351783 557 60 Risk Risk NNP 10_1101-2020_10_26_351783 557 61 � � NNP 10_1101-2020_10_26_351783 557 62 Risk Risk NNP 10_1101-2020_10_26_351783 557 63 � � NNP 10_1101-2020_10_26_351783 557 64 Risk Risk NNP 10_1101-2020_10_26_351783 557 65 a a DT 10_1101-2020_10_26_351783 557 66 c c NN 10_1101-2020_10_26_351783 557 67 b b NN 10_1101-2020_10_26_351783 557 68 Module Module NNP 10_1101-2020_10_26_351783 557 69 enrichments enrichment NNS 10_1101-2020_10_26_351783 557 70 1 1 CD 10_1101-2020_10_26_351783 557 71 2 2 CD 10_1101-2020_10_26_351783 557 72 3 3 CD 10_1101-2020_10_26_351783 557 73 4 4 CD 10_1101-2020_10_26_351783 557 74 Risk risk NN 10_1101-2020_10_26_351783 557 75 factor factor NN 10_1101-2020_10_26_351783 557 76 datasets dataset VBZ 10_1101-2020_10_26_351783 557 77 -log10 -log10 NNP 10_1101-2020_10_26_351783 557 78 P p NN 10_1101-2020_10_26_351783 557 79 α α NN 10_1101-2020_10_26_351783 557 80 = = NNS 10_1101-2020_10_26_351783 557 81 .05 .05 CD 10_1101-2020_10_26_351783 557 82 1 1 CD 10_1101-2020_10_26_351783 557 83 2 2 CD 10_1101-2020_10_26_351783 557 84 3 3 CD 10_1101-2020_10_26_351783 557 85 4 4 CD 10_1101-2020_10_26_351783 557 86 Validation validation NN 10_1101-2020_10_26_351783 557 87 dataset dataset NN 10_1101-2020_10_26_351783 557 88 -log10 -log10 NNP 10_1101-2020_10_26_351783 557 89 P p NN 10_1101-2020_10_26_351783 557 90 α α NN 10_1101-2020_10_26_351783 557 91 = = SYM 10_1101-2020_10_26_351783 557 92 .05 .05 NFP 10_1101-2020_10_26_351783 557 93 NA NA NNP 10_1101-2020_10_26_351783 557 94 NA NA NNP 10_1101-2020_10_26_351783 557 95 NA NA NNP 10_1101-2020_10_26_351783 557 96 7.4 7.4 CD 10_1101-2020_10_26_351783 557 97 � � NN 10_1101-2020_10_26_351783 557 98 Risk risk NN 10_1101-2020_10_26_351783 557 99 ( ( -LRB- 10_1101-2020_10_26_351783 557 100 which which WDT 10_1101-2020_10_26_351783 557 101 was be VBD 10_1101-2020_10_26_351783 557 102 not not RB 10_1101-2020_10_26_351783 557 103 certified certify VBN 10_1101-2020_10_26_351783 557 104 by by IN 10_1101-2020_10_26_351783 557 105 peer peer NN 10_1101-2020_10_26_351783 557 106 review review NN 10_1101-2020_10_26_351783 557 107 ) ) -RRB- 10_1101-2020_10_26_351783 557 108 is be VBZ 10_1101-2020_10_26_351783 557 109 the the DT 10_1101-2020_10_26_351783 557 110 author author NN 10_1101-2020_10_26_351783 557 111 / / SYM 10_1101-2020_10_26_351783 557 112 funder funder NN 10_1101-2020_10_26_351783 557 113 . . . 10_1101-2020_10_26_351783 558 1 All all DT 10_1101-2020_10_26_351783 558 2 rights right NNS 10_1101-2020_10_26_351783 558 3 reserved reserve VBD 10_1101-2020_10_26_351783 558 4 . . . 10_1101-2020_10_26_351783 559 1 No no DT 10_1101-2020_10_26_351783 559 2 reuse reuse NN 10_1101-2020_10_26_351783 559 3 allowed allow VBN 10_1101-2020_10_26_351783 559 4 without without IN 10_1101-2020_10_26_351783 559 5 permission permission NN 10_1101-2020_10_26_351783 559 6 . . . 10_1101-2020_10_26_351783 560 1 The the DT 10_1101-2020_10_26_351783 560 2 copyright copyright NN 10_1101-2020_10_26_351783 560 3 holder holder NN 10_1101-2020_10_26_351783 560 4 for for IN 10_1101-2020_10_26_351783 560 5 this this DT 10_1101-2020_10_26_351783 560 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 560 7 version version NN 10_1101-2020_10_26_351783 560 8 posted post VBD 10_1101-2020_10_26_351783 560 9 January January NNP 10_1101-2020_10_26_351783 560 10 6 6 CD 10_1101-2020_10_26_351783 560 11 , , , 10_1101-2020_10_26_351783 560 12 2021 2021 CD 10_1101-2020_10_26_351783 560 13 . . . 10_1101-2020_10_26_351783 560 14 ; ; : 10_1101-2020_10_26_351783 560 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 560 16 : : : 10_1101-2020_10_26_351783 560 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 560 18 preprint preprint NN 10_1101-2020_10_26_351783 560 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 CC 10_1101-2020_10_26_351783 560 20 33 33 CD 10_1101-2020_10_26_351783 560 21 module module JJ 10_1101-2020_10_26_351783 560 22 genes gene NNS 10_1101-2020_10_26_351783 560 23 in in IN 10_1101-2020_10_26_351783 560 24 the the DT 10_1101-2020_10_26_351783 560 25 top top JJ 10_1101-2020_10_26_351783 560 26 1,000 1,000 CD 10_1101-2020_10_26_351783 560 27 DMGs dmg NNS 10_1101-2020_10_26_351783 560 28 in in IN 10_1101-2020_10_26_351783 560 29 risk risk NN 10_1101-2020_10_26_351783 560 30 factor factor NN 10_1101-2020_10_26_351783 560 31 datasets dataset NNS 10_1101-2020_10_26_351783 560 32 and and CC 10_1101-2020_10_26_351783 560 33 independent independent JJ 10_1101-2020_10_26_351783 560 34 risk risk NN 10_1101-2020_10_26_351783 560 35 factor factor NN 10_1101-2020_10_26_351783 560 36 methylation methylation NN 10_1101-2020_10_26_351783 560 37 dataset dataset NN 10_1101-2020_10_26_351783 560 38 ( ( -LRB- 10_1101-2020_10_26_351783 560 39 see see VB 10_1101-2020_10_26_351783 560 40 Methods method NNS 10_1101-2020_10_26_351783 560 41 ) ) -RRB- 10_1101-2020_10_26_351783 560 42 shown show VBN 10_1101-2020_10_26_351783 560 43 as as IN 10_1101-2020_10_26_351783 560 44 Fisher Fisher NNP 10_1101-2020_10_26_351783 560 45 exact exact JJ 10_1101-2020_10_26_351783 560 46 test test NN 10_1101-2020_10_26_351783 560 47 P p NN 10_1101-2020_10_26_351783 560 48 - - HYPH 10_1101-2020_10_26_351783 560 49 values value NNS 10_1101-2020_10_26_351783 560 50 ( ( -LRB- 10_1101-2020_10_26_351783 560 51 threshold threshold NN 10_1101-2020_10_26_351783 560 52 α=0.05 α=0.05 NNP 10_1101-2020_10_26_351783 560 53 ) ) -RRB- 10_1101-2020_10_26_351783 560 54 . . . 10_1101-2020_10_26_351783 561 1 ( ( -LRB- 10_1101-2020_10_26_351783 561 2 c c NN 10_1101-2020_10_26_351783 561 3 ) ) -RRB- 10_1101-2020_10_26_351783 561 4 Visualization visualization NN 10_1101-2020_10_26_351783 561 5 of of IN 10_1101-2020_10_26_351783 561 6 the the DT 10_1101-2020_10_26_351783 561 7 module module NN 10_1101-2020_10_26_351783 561 8 . . . 10_1101-2020_10_26_351783 562 1 Nodes node NNS 10_1101-2020_10_26_351783 562 2 ( ( -LRB- 10_1101-2020_10_26_351783 562 3 module module JJ 10_1101-2020_10_26_351783 562 4 genes gene NNS 10_1101-2020_10_26_351783 562 5 ) ) -RRB- 10_1101-2020_10_26_351783 562 6 are be VBP 10_1101-2020_10_26_351783 562 7 arranged arrange VBN 10_1101-2020_10_26_351783 562 8 in in IN 10_1101-2020_10_26_351783 562 9 functional functional JJ 10_1101-2020_10_26_351783 562 10 clusters cluster NNS 10_1101-2020_10_26_351783 562 11 according accord VBG 10_1101-2020_10_26_351783 562 12 to to IN 10_1101-2020_10_26_351783 562 13 their -PRON- PRP$ 10_1101-2020_10_26_351783 562 14 overrepresented overrepresente VBN 10_1101-2020_10_26_351783 562 15 GO GO NNP 10_1101-2020_10_26_351783 562 16 terms term NNS 10_1101-2020_10_26_351783 562 17 . . . 10_1101-2020_10_26_351783 563 1 Genes gene NNS 10_1101-2020_10_26_351783 563 2 with with IN 10_1101-2020_10_26_351783 563 3 a a DT 10_1101-2020_10_26_351783 563 4 known know VBN 10_1101-2020_10_26_351783 563 5 association association NN 10_1101-2020_10_26_351783 563 6 to to IN 10_1101-2020_10_26_351783 563 7 MS MS NNP 10_1101-2020_10_26_351783 563 8 are be VBP 10_1101-2020_10_26_351783 563 9 marked mark VBN 10_1101-2020_10_26_351783 563 10 with with IN 10_1101-2020_10_26_351783 563 11 a a DT 10_1101-2020_10_26_351783 563 12 blue blue JJ 10_1101-2020_10_26_351783 563 13 circle circle NN 10_1101-2020_10_26_351783 563 14 . . . 10_1101-2020_10_26_351783 564 1 Node Node NNP 10_1101-2020_10_26_351783 564 2 colors color NNS 10_1101-2020_10_26_351783 564 3 display display VBP 10_1101-2020_10_26_351783 564 4 the the DT 10_1101-2020_10_26_351783 564 5 associations association NNS 10_1101-2020_10_26_351783 564 6 to to IN 10_1101-2020_10_26_351783 564 7 an an DT 10_1101-2020_10_26_351783 564 8 MS MS NNP 10_1101-2020_10_26_351783 564 9 risk risk NN 10_1101-2020_10_26_351783 564 10 factor factor NN 10_1101-2020_10_26_351783 564 11 for for IN 10_1101-2020_10_26_351783 564 12 which which WDT 10_1101-2020_10_26_351783 564 13 the the DT 10_1101-2020_10_26_351783 564 14 module module NN 10_1101-2020_10_26_351783 564 15 is be VBZ 10_1101-2020_10_26_351783 564 16 significantly significantly RB 10_1101-2020_10_26_351783 564 17 enriched enrich VBN 10_1101-2020_10_26_351783 564 18 ( ( -LRB- 10_1101-2020_10_26_351783 564 19 red red JJ 10_1101-2020_10_26_351783 564 20 , , , 10_1101-2020_10_26_351783 564 21 alcohol alcohol NN 10_1101-2020_10_26_351783 564 22 use use NN 10_1101-2020_10_26_351783 564 23 ; ; : 10_1101-2020_10_26_351783 564 24 green green JJ 10_1101-2020_10_26_351783 564 25 , , , 10_1101-2020_10_26_351783 564 26 high high JJ 10_1101-2020_10_26_351783 564 27 BMI bmi NN 10_1101-2020_10_26_351783 564 28 ; ; : 10_1101-2020_10_26_351783 564 29 yellow yellow NN 10_1101-2020_10_26_351783 564 30 , , , 10_1101-2020_10_26_351783 564 31 smoking smoking NN 10_1101-2020_10_26_351783 564 32 ; ; : 10_1101-2020_10_26_351783 564 33 purple purple JJ 10_1101-2020_10_26_351783 564 34 , , , 10_1101-2020_10_26_351783 564 35 low low JJ 10_1101-2020_10_26_351783 564 36 sun sun NN 10_1101-2020_10_26_351783 564 37 exposure exposure NN 10_1101-2020_10_26_351783 564 38 ; ; : 10_1101-2020_10_26_351783 564 39 light light JJ 10_1101-2020_10_26_351783 564 40 blue blue NN 10_1101-2020_10_26_351783 564 41 , , , 10_1101-2020_10_26_351783 564 42 EBV EBV NNP 10_1101-2020_10_26_351783 564 43 infection infection NN 10_1101-2020_10_26_351783 564 44 ; ; : 10_1101-2020_10_26_351783 564 45 grey grey NNP 10_1101-2020_10_26_351783 564 46 , , , 10_1101-2020_10_26_351783 564 47 no no DT 10_1101-2020_10_26_351783 564 48 association association NN 10_1101-2020_10_26_351783 564 49 ) ) -RRB- 10_1101-2020_10_26_351783 564 50 . . . 10_1101-2020_10_26_351783 565 1 Edges edge NNS 10_1101-2020_10_26_351783 565 2 were be VBD 10_1101-2020_10_26_351783 565 3 extracted extract VBN 10_1101-2020_10_26_351783 565 4 from from IN 10_1101-2020_10_26_351783 565 5 the the DT 10_1101-2020_10_26_351783 565 6 STRINGdb STRINGdb NNP 10_1101-2020_10_26_351783 565 7 v11 v11 NN 10_1101-2020_10_26_351783 565 8 human human JJ 10_1101-2020_10_26_351783 565 9 PPI PPI NNP 10_1101-2020_10_26_351783 565 10 network network NN 10_1101-2020_10_26_351783 565 11 of of IN 10_1101-2020_10_26_351783 565 12 experimentally experimentally RB 10_1101-2020_10_26_351783 565 13 validated validate VBN 10_1101-2020_10_26_351783 565 14 interactions interaction NNS 10_1101-2020_10_26_351783 565 15 ( ( -LRB- 10_1101-2020_10_26_351783 565 16 confidence confidence NN 10_1101-2020_10_26_351783 565 17 score score NN 10_1101-2020_10_26_351783 565 18 > > XX 10_1101-2020_10_26_351783 565 19 700 700 CD 10_1101-2020_10_26_351783 565 20 ) ) -RRB- 10_1101-2020_10_26_351783 565 21 . . . 10_1101-2020_10_26_351783 566 1 SUPPLEMENTARY supplementary NN 10_1101-2020_10_26_351783 566 2 MATERIALS material NNS 10_1101-2020_10_26_351783 566 3 Supplementary Supplementary NNP 10_1101-2020_10_26_351783 566 4 Table Table NNP 10_1101-2020_10_26_351783 566 5 1 1 CD 10_1101-2020_10_26_351783 566 6 : : : 10_1101-2020_10_26_351783 566 7 All all DT 10_1101-2020_10_26_351783 566 8 case case NN 10_1101-2020_10_26_351783 566 9 - - HYPH 10_1101-2020_10_26_351783 566 10 control control NN 10_1101-2020_10_26_351783 566 11 comparisons comparison NNS 10_1101-2020_10_26_351783 566 12 used use VBN 10_1101-2020_10_26_351783 566 13 in in IN 10_1101-2020_10_26_351783 566 14 the the DT 10_1101-2020_10_26_351783 566 15 Transcriptomic Transcriptomic NNP 10_1101-2020_10_26_351783 566 16 and and CC 10_1101-2020_10_26_351783 566 17 Methylomic methylomic JJ 10_1101-2020_10_26_351783 566 18 benchmarks benchmark NNS 10_1101-2020_10_26_351783 566 19 . . . 10_1101-2020_10_26_351783 567 1 Supplementary supplementary JJ 10_1101-2020_10_26_351783 567 2 Table table NN 10_1101-2020_10_26_351783 567 3 2 2 CD 10_1101-2020_10_26_351783 567 4 : : : 10_1101-2020_10_26_351783 567 5 All all DT 10_1101-2020_10_26_351783 567 6 case case NN 10_1101-2020_10_26_351783 567 7 - - HYPH 10_1101-2020_10_26_351783 567 8 control control NN 10_1101-2020_10_26_351783 567 9 comparisons comparison NNS 10_1101-2020_10_26_351783 567 10 used use VBN 10_1101-2020_10_26_351783 567 11 in in IN 10_1101-2020_10_26_351783 567 12 the the DT 10_1101-2020_10_26_351783 567 13 MS MS NNP 10_1101-2020_10_26_351783 567 14 use use NN 10_1101-2020_10_26_351783 567 15 case case NN 10_1101-2020_10_26_351783 567 16 benchmark benchmark JJ 10_1101-2020_10_26_351783 567 17 . . . 10_1101-2020_10_26_351783 568 1 Supplementary supplementary JJ 10_1101-2020_10_26_351783 568 2 Table table NN 10_1101-2020_10_26_351783 568 3 3 3 CD 10_1101-2020_10_26_351783 568 4 : : : 10_1101-2020_10_26_351783 568 5 All all DT 10_1101-2020_10_26_351783 568 6 Methods Methods NNPS 10_1101-2020_10_26_351783 568 7 implemented implement VBN 10_1101-2020_10_26_351783 568 8 in in IN 10_1101-2020_10_26_351783 568 9 the the DT 10_1101-2020_10_26_351783 568 10 benchmark benchmark NN 10_1101-2020_10_26_351783 568 11 . . . 10_1101-2020_10_26_351783 569 1 ( ( -LRB- 10_1101-2020_10_26_351783 569 2 which which WDT 10_1101-2020_10_26_351783 569 3 was be VBD 10_1101-2020_10_26_351783 569 4 not not RB 10_1101-2020_10_26_351783 569 5 certified certify VBN 10_1101-2020_10_26_351783 569 6 by by IN 10_1101-2020_10_26_351783 569 7 peer peer NN 10_1101-2020_10_26_351783 569 8 review review NN 10_1101-2020_10_26_351783 569 9 ) ) -RRB- 10_1101-2020_10_26_351783 569 10 is be VBZ 10_1101-2020_10_26_351783 569 11 the the DT 10_1101-2020_10_26_351783 569 12 author author NN 10_1101-2020_10_26_351783 569 13 / / SYM 10_1101-2020_10_26_351783 569 14 funder funder NN 10_1101-2020_10_26_351783 569 15 . . . 10_1101-2020_10_26_351783 570 1 All all DT 10_1101-2020_10_26_351783 570 2 rights right NNS 10_1101-2020_10_26_351783 570 3 reserved reserve VBD 10_1101-2020_10_26_351783 570 4 . . . 10_1101-2020_10_26_351783 571 1 No no DT 10_1101-2020_10_26_351783 571 2 reuse reuse NN 10_1101-2020_10_26_351783 571 3 allowed allow VBN 10_1101-2020_10_26_351783 571 4 without without IN 10_1101-2020_10_26_351783 571 5 permission permission NN 10_1101-2020_10_26_351783 571 6 . . . 10_1101-2020_10_26_351783 572 1 The the DT 10_1101-2020_10_26_351783 572 2 copyright copyright NN 10_1101-2020_10_26_351783 572 3 holder holder NN 10_1101-2020_10_26_351783 572 4 for for IN 10_1101-2020_10_26_351783 572 5 this this DT 10_1101-2020_10_26_351783 572 6 preprintthis preprintthis NN 10_1101-2020_10_26_351783 572 7 version version NN 10_1101-2020_10_26_351783 572 8 posted post VBD 10_1101-2020_10_26_351783 572 9 January January NNP 10_1101-2020_10_26_351783 572 10 6 6 CD 10_1101-2020_10_26_351783 572 11 , , , 10_1101-2020_10_26_351783 572 12 2021 2021 CD 10_1101-2020_10_26_351783 572 13 . . . 10_1101-2020_10_26_351783 572 14 ; ; : 10_1101-2020_10_26_351783 572 15 https://doi.org/10.1101/2020.10.26.351783doi https://doi.org/10.1101/2020.10.26.351783doi ADD 10_1101-2020_10_26_351783 572 16 : : : 10_1101-2020_10_26_351783 572 17 bioRxiv biorxiv VB 10_1101-2020_10_26_351783 572 18 preprint preprint NN 10_1101-2020_10_26_351783 572 19 https://doi.org/10.1101/2020.10.26.351783 https://doi.org/10.1101/2020.10.26.351783 XX