Identifying Regulatory Subnetworks for a Set of Genes

• DOI: 10.1074/mcp.m400110-mcp200
• Publication Date: 2005-02-19T01:13:25Z
• Authors: Michelle S. Scott; Theodore Perkins; Scott Bunnell; François Pepin; David Y. Thomas; Michael Hallett
• Keywords: Chromatin immunoprecipitation; Gene regulatory network

High throughput genomic/proteomic strategies, such as microarray studies, drug screens, and genetic often produce a list of genes that are believed to be important for one or more reasons. Unfortunately it is difficult discern meaningful biological relationships from lists. This study presents new bioinformatic approach can used identify regulatory subnetworks lists significant proteins. We demonstrate the utility this using an interaction network yeast constructed BIND, TRANSFAC, SCPD, chromatin immunoprecipitation (ChIP)-Chip data bases well known metabolic pathways differential expression experiments. The accurately rediscovers elements heat shock response gluconeogenesis, galactose, glycolysis, glucose fermentation in yeast. also find evidence supporting previous conjecture approximately half enzymes pathway transcriptionally co-regulated. Finally we previously unknown connection between GAL80 diauxic shift