Finding potential TF for a specific gene

[Lb B]

Hello,

I am sorry for the dumb question, but I am just a beginner in lab work and in in silico analysis.

I am interested in finding a list of potential transcription factors for a specific gene (human).

I am searching in the promoter region, around 5000bp upstream the first exon (and first exon included).

Should I include all the homo sapiens profiles available (810) and then use my FASTA sequence to search? (I know I would have to break down in 3000bp or even less - as I am getting the problem in loading the webpage as bad gateway).

I would just like to know if I am doing the right thing. For sure my list of potential TF will be long, but I will screen for TF based in the literature later on.

Thank you.

Lisia 

[Anthony Mathelier]

Hello,

If you are looking for some potential TFBSs in a given set of regions, I suggest that you download the set of predicted TFBSs from JASPAR (see http://jaspar.genereg.net/genome-tracks/). These are lenient predictions; if you are interested in more robust predictions combining PFMs from JASPAR with ChIP-seq data, you could use our TFBS predictions stored in UniBind (https://unibind.uio.no/).

Hope it helps.
Best
AM

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