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Transcription Factor Binding Sites

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!

sequence-search tfbs
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updated by Ram Ram • written by andrew.j.skelton73 andrew.j.skelton73

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/

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updated by Ram Ram • written by roy.granit roy.granit

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

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written by Ying W Ying W

3 answers

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

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written by hpmcwill hpmcwill

you can consult UCSC genome browser too.

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written by noor.us.sehar941 • noor.us.sehar941

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:

• 0 views • link
written by robinvanderlee • robinvanderlee

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