Transcription Factor Binding Sites

Question

[andrew.j.skelton73]

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!

[roy.granit]

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/

[Ying W]

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

Answer 1

[hpmcwill]

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

Answer 2

[noor.us.sehar941]

you can consult UCSC genome browser too.

Answer 3

[robinvanderlee]

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:

• http://jaspar.genereg.net/genome-tracks/
• http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=637724977_mCbJ8XvftLprsVMF8MFL6cSXJXfz&c=chr1&g=hub_186875_JasparTFBS
• http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2018/