Regulatory Motifs cMonkey Network

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values).

Columns:

• Title: Name of the regulatory motif identified by cMonkey and linked to motif's details page
• Logo: is a graphical representation of the sequence conservation of DNA
• e-value: Motif e-value is an indicative of the motif co-occurences between the members of the module. Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.
• Number of sites: Number of genes in a given module that includes identified motif in the upstream region
• Length: Number of nucleotide bases in the motif logo
• Motif Bicluster: Regulatory module/bicluster that includes given motif.
• : Clicking on the icon will display detailed motif information in an overlay window.

Reference: Reiss, D. J., Baliga N. S., & Bonneau R. (2006). Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC bioinformatics. 7, 280