Linking Two Gene Activity via Transcription Factors similarities
1
0
Entering edit mode
7 weeks ago
qmarulfiz ▴ 60

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!

mRNA Translation GeneExpression TranscriptionFactor • 1.5k views
ADD COMMENT
1
Entering edit mode
7 weeks ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 2616 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6