A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes

Background: Observed co-expression of a group of genes is frequently attributed to co-regulation by shared transcription factors. This assumption has led to the hypothesis that promoters of co-expressed genes should share common regulatory motifs, which forms the basis for numerous computational tools that search for these motifs. While frequently explored for yeast, the validity of the underlying hypothesis has not been assessed systematically in mammals. This demonstrates the need for a systematic and quantitative evaluation to what degree co-expressed genes share over-represented motifs for mammals. Results: We identified 33 experiments for human and mouse in the ArrayExpress Database where transcription factors were manipulated and which exhibited a significant number of differentially expressed genes. We checked for over-representation of transcription factor binding sites in up- or down-regulated genes using the over-representation analysis tool oPOSSUM. In 25 out of 33 experime...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Guofeng Meng, Axel Mosig, Martin Vingron
• Keywords: BMCBI 2010, Expressed Genes, Regulatory Motifs, Transcription Factors