Linking Two Gene Activity via Transcription Factors similarities

Question

[qmarulfiz]

Let say I suspect Gene A and Gene B of mouse share similar Transcription Factor.

What should I do to prove this?

From my limited reading, I manage to obtain a list of TF from PROMO website for Gene A and Gene B by simply input 1kb sequence of both genes 5'-region.

How should I go on to prove this? What data I need or relevant enough to put in scientific publication to justify my suspicion?

*Background Information Limited metabolite data seem to suggest Knock Out of Gene A increase Gene B pathway activity. Of course best way to prove this is gene expression of these 2 genes. But with limited fund and time, I try to explore other possibilities first.

Thank you again everyone for reading helping me to understand bioinformatic area!

Answer 1

[Alex Reynolds]

You can get use a computational tool like FIMO to find putative TF binding sites in proximal promoters, given known or published TF MEME tables. If you get the same TF hit under some reasonable p-value threshold, then that might be evidence. This is suggestive but not sufficient. Using a tool like bedmap to associate a transcription factor's ChIP-seq peaks to the proximal promoters for the genes of interest would add to that evidence. If you have knock-down or knock-out experiments that prevent that TF from binding and you get a significant change in expression, that could be additional evidence.