id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-002139-zlqh436d	Chasman, Deborah	Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens	2016-07-12		.txt	text/plain	14786	655	42	This integrated regulatory module network enabled (3) prioritization of regulators for validation of their ability to modulate viral replication, (4) an examination of network dynamics across virus treatments, and (5) a further integration with external protein-protein interactions to predict directed physical connections between the mRNA, protein-based regulators and known influenza host response genes. We used a recently developed network inference algorithm, 'Modular regulatory network learning with per gene information' (MERLIN [22] ) that uses genome-wide mRNA levels from multiple biological samples (time points or treatments) to predict regulatory relationships between regulators (e.g. transcription factors or signaling proteins) and target genes. Based on a hypergeometric test with FDR correction (FDR<0.05), 32 out of the 41 human Calu-3 modules (40 of 56 mouse modules) exhibited enrichment in one or more of the annotation categories representing Gene Ontology processes, KEGG pathways, and influenza related gene sets identified from 10 high-throughput RNAi studies and viral-host protein-protein interaction screens (Fig 2, S1 Fig, S1 Table, S2 Table) .	./cache/cord-002139-zlqh436d.txt	./txt/cord-002139-zlqh436d.txt