Hi David,

currently this is done through "homology Wizard, by right click mouse on any set of objects (from search, groups, network, experiment, etc.) and chose "Homology Wizard" that searches for homologs of your input gene list, binding sites, it contains multi-experiment search for co-expressed genes and builds gene regulatory modular network.

We think, this is too much for "Homology Wizard" and we are currently dis-segmenting it into three separate wizards:
1) Homology Wizard- that will just search for homologs of your gene list in multiple organisms with different levels of homology stringency
2) Binding Sites Wizard- that will allow to search binding sites, and to visualize them in the Genome Browser
to comparatively navigate through conserved binding sites
3) Gene Regulatory Modules Wizard- that in addition to all functionality included in previous Wizard will allow to search co-expression data in multiple microarray experiment using filters on cell/tissue type, organism, etc. and build gene regulatory modular network integrating binding motifs, co-expression and interaction data.

Lets us know if you have questions, or any additional features and ideas on implementing this.

Thanks!

Update:

We use transcription matrices from TRANSFAC, JASPAR and other sources see the complete list of integrated data sources for regulatory data at http://biologicalnetworks.org/Database/tut5.php

Thanks.