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?
2 answers
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.
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/
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