find transcription factor

Question

[??]

Hi,

I am now trying to find some transcription factors among all the genes that are regulated by certain drug treatment. What kind of softwares are the most useful tool to help me find TFs. thanks

Answer 1

[Alex Reynolds]

You could use FIMO to search for TF sites across your genome, given a TF database such as JASPAR, TRANSFAC, UniPROBE, etc.

Once you have the predicted TF sites, you can use set operations tools like BEDOPS to find TF sites that overlap (drug target) gene annotations, predicted promoters, ChIP-seq data, etc. which are converted to sorted BED files.

[??]

thanks!

[bharata1803]

Hello, actually I have the same problem. Thank you for your information. Also, I want to ask about transcription factor which is listed in genecards website, for example this http://v4.genecards.org/cgi-bin/carddisp.pl?gene=UGT1A1

I can see there is a list of regukatory element and then see all link, which is linked to this link

First, is TF can be that many for only one gene?

Second, with the software you mention, I'm a bit confused with predicted TF sites. So, is it database for only prediction or the acctual TF of genes?

Thank you.