Question: Transcription Factor Binding Sites
1
gravatar for andrew.j.skelton73
4.4 years ago by
London
andrew.j.skelton735.6k wrote:

Hi, 

I'm trying to find what transcription factor binding sites are within or around a set of candidate genes. So far I've been using a ChIP Seq ENCODE track as a reference but I was wondering if there were any other computational methods or databases of known human transcription factor binding sites? I've tried searching for this information in biomaRt too, but no such look. 

Any suggestions?

Thanks!

ADD COMMENTlink modified 17 months ago by robinvanderlee10 • written 4.4 years ago by andrew.j.skelton735.6k
1

Note you can also extract these binding sites from ENCODE via galaxy to do this in a more comprehensive way. Maybe the meme suite can help you out a bit:

http://meme.nbcr.net/meme/

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by roy.granit790
1

are you looking for motifs or binding sites? binding sites will differ by cell line / condition

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Ying W3.9k
3
gravatar for hpmcwill
4.4 years ago by
hpmcwill1.1k
United Kingdom
hpmcwill1.1k wrote:

Try having a look at some of the transcription factor databases (e.g. JASPAR, TRANSFAC, etc.).

ADD COMMENTlink written 4.4 years ago by hpmcwill1.1k
1
gravatar for noor.us.sehar941
4.4 years ago by
Pakistan
noor.us.sehar94110 wrote:

you can consult UCSC genome browser too.

ADD COMMENTlink written 4.4 years ago by noor.us.sehar94110
1
gravatar for robinvanderlee
17 months ago by
Vancouver, Canada
robinvanderlee10 wrote:

If anyone would ever still come across this question: we now provide JASPAR TF binding site predictions for a number of organisms as genome tracks, including at UCSC.

More information:

ADD COMMENTlink written 17 months ago by robinvanderlee10
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