Tool For Quickly Establishing If Two Genes May Be Co-Regulated

Question

[Paul]

I've identified two human genes with very similar expression profiles and I wish to identify if there is evidence, based on their promoter sequences, that they are co-regulated by a particular transcription factor and if so what that transcription factor might be.

My question is, is there any tool available that will allow me to quickly and easily do this?

Answer 1

[Ying W]

What I would do is take the promoter sequence of both of these genes and do a pairwise alignment. Look for regions of similarity (4bp+) and look for conservation in these candidate regions (higher chance this is a transcription factor binding site). Then I would take this small sequence and look in a motif database like JASPAR to see if there is a transcription factor that binds this sequence.

Answer 2

[Jean-Karim Heriche]

You could use any number of tools designed for transcription factor binding site identification/prediction. For example, you could scan your sequences with profiles from the JASPAR database: http://jaspar.cgb.ki.se/