Description

This track shows predicted transcription factor binding sites based on sequence similarities upstream of coordinately expressed genes.

In dense display mode the gold areas indicate the extent of the area searched for binding sites; black boxes indicate the actual binding sites. In other modes the gold areas disappear and only the binding sites are displayed. Clicking on a particular predicted binding site displays a page that shows the sequence motif associated with the predicted transcription factor and the sequence at the predicted binding site. Where known motifs have been identified by this method, they are named; otherwise, they are assigned a motif number.

Methods

This analysis was performed according to Genome-wide discovery of transcriptional modules from DNA sequence and gene expression on various pre-existing microarray datasets. A regulatory module is comprised of a set of genes predicted to be regulated by the same combination of DNA sequence motifs. The predictions are based on the co-expression of the set of genes in the module and on the appearance of common combinations of motifs in the upstream regions of genes assigned to the same module.

Credits

Thanks to Eran Segal for providing the data analysis that forms the basis for this track. The display was programmed by Jim Kent.

References

Segal E, Yelensky R, Koller D. Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics. 2003;19 Suppl 1:i273-82. PMID: 12855470