title: A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes.
abstract: 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 experiments, this procedure identified the binding matrices of the affected transcription factors. We also carried out de novo prediction of regulatory motifs shared by differentially expressed genes. Again, the detected motifs shared significant similarity with the matrices of the affected transcription factors.
  
  
  CONCLUSIONS
  Our results support the claim that functional regulatory motifs are over-represented in sets of differentially expressed genes and that they can be detected with computational methods.
authors.affiliation: CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, 320 Yue Yang Road, 200031, Shanghai, China. gfmeng@picb.ac.cn
authors.forename: Guofeng
authors.initials: G
authors.lastname: Meng
authors.forename: Axel
authors.initials: A
authors.lastname: Mosig
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D011401:Promoter Regions, Genetic / Q000235:genetics*