id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-048345-m56agj4z	Reddy, Timothy E.	Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABA(A) receptor subunit genes	2007-01-03		.txt	text/plain	5445	290	40	title: Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABA(A) receptor subunit genes We evaluate the efficacy of our approach using known examples of binding and regulation in yeast and experimentally testing predicted TF-binding sites upstream of the subunit genes coding for the heteromeric mammalian neurotransmitter receptor system, the type A g-aminobutyric acid receptor (GABA A R). In the current study, we test the ability of positional clustering to detect known TF-binding sites in a series of increasingly noisy sets of yeast promoters, and found marked improvement in the percentage of correct predictions over Gibbs sampling alone. We also present de novo predictions of TF-binding sites in promoter regions of GABA A receptor subunit genes (GABRs) whose expression is altered (either up-regulated or down-regulated) in an animal model of temporal lobe epilepsy (35) . Using positional clustering, we predicted 13 TF-binding sites upstream of GABA A receptor subunit genes ( Table 1) .	./cache/cord-048345-m56agj4z.txt	./txt/cord-048345-m56agj4z.txt