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 d

SUBMITTER: Meng G 

PROVIDER: S-EPMC3098066 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature