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- Title
Functional inference from non-random distributions of conserved predicted transcription factor binding sites.
- Authors
Dieterich, Christoph; Rahmann, Sven; Vingron, Martin
- Abstract
Our understanding of how genes are regulated in a concerted fashion is still limited. Especially, complex phenomena like cell cycle regulation in multicellular organisms are poorly understood. Therefore, we investigated conserved predicted transcription factor binding sites (TFBSs) in man-mouse upstream regions of genes that can be associated to a particular cell cycle phase in HeLa cells. TFBSs were predicted from selected binding site motifs (represented by position weight matrices, PWMs) based on a statistical approach. A regulatory role for a transcription factor is more probable if its predicted TFBSs are enriched in upstream regions of genes, that are associated with a subset of cell cycle phases. We tested for this association by computing exact P-values for the observed phase distributions under the null distribution defined by the relative amount of conserved upstream sequence of genes per cell cycle phase. We considered non-exonic and 5'-untranslated region (5'-UTR) binding sites separately and corrected for multiple testing by taking the false discovery rate into account.
- Publication
Bioinformatics (Oxford, England), 2004, Vol 20 Suppl 1, pi109
- ISSN
1367-4811
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/bth908