Prioritization of gene regulatory interactions from large-scale modules in yeast

Background: The identification of groups of co-regulated genes and their transcription factors, called transcriptional modules, has been a focus of many studies about biological systems. While methods have been developed to derive numerous modules from genome-wide data, individual links between regulatory proteins and target genes still need experimental verification. In this work, we aim to prioritize regulator-target links within transcriptional modules based on three types of large-scale data sources. Results: Starting with putative transcriptional modules from ChIP-chip data, we first derive modules in which target genes show both expression and function coherence. The most reliable regulatory links between transcription factors and target genes are established by identifying intersection of target genes in coherent modules for each enriched functional category. Using a combination of genome-wide yeast data in normal growth conditions and two different reference datasets, we show ...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Ho-Joon Lee, Thomas Manke, Ricardo Bringas, Martin Vingron
• Keywords: BMCBI 2008, Regulatory Interactions, Transcription Factors, Transcriptional Modules