Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors

Background: Evolutionary conservation has been used successfully to help identify cis-acting DNA regions that are important in regulating tissue-specific gene expression. Motivated by increasing evidence that some DNA regulatory regions are not evolutionary conserved, we have developed an approach for cis-regulatory region identification that does not rely upon evolutionary sequence conservation. Results: The conservation-independent approach is based on an empirical potential energy between interacting transcription factors (TFs). In this analysis, the potential energy is defined as a function of the number of TF interactions in a genomic region and the strength of the interactions. By identifying sets of interacting TFs, the analysis locates regions enriched with the binding sites of these interacting TFs. We applied this approach to 30 human tissues and identified 6232 putative cis-regulatory modules (CRMs) regulating 2130 tissue-specific genes. Interestingly, some genes appear to ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Xueping Yu, Jimmy J. Lin, Donald J. Zack, Jiang Qian
• Keywords: BMCBI 2007, DNA Regulatory Regions, Regulatory Regions, Tissue-specific Genes