Question: How To Obtain Encode Tfbs Using The Ucsc Genome Browser
gravatar for Linda
8.2 years ago by
Linda160 wrote:

I am interested in finding all known Transcription Factor Binding sites for a list of genes from the ENCODE dataset. How could one automate that? From the tables it appears that each TF has its own table. Thus, I could obtain promoters for my set of genes and find its intersection with the table of the TF in question. But the number of tables is rather large and the names do not follow any convention that I could discern. Is there a way to automate this process?

binding encode transcription • 11k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 8.2 years ago by Linda160
gravatar for Mikael Huss
8.2 years ago by
Mikael Huss4.6k
Mikael Huss4.6k wrote:

It's possible that this can be done with table intersections, but personally I would simply download all the files from e g the Yale lab ( and the Hudson Alpha lab ( - these are both for hg18 by the way - and there are other labs as well. Then I would look at the narrowPeak files, which contain predicted TF binding sites based on the ChIP-seq data.

ADD COMMENTlink written 8.2 years ago by Mikael Huss4.6k

Hey Mikael, How to cite it if I do the intersect by these two datast?

ADD REPLYlink written 3.3 years ago by Shicheng Guo7.5k

I agree with Mikael, doing this using UCSC data would be easier locally, by downloading human ChIP at and using overlapSelect from the UCSC toolkit:

ADD REPLYlink written 8.2 years ago by Casey Bergman18k
gravatar for Casey Bergman
8.2 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

If you are interested in large-scale TFBS data in general but not ENCODE data per se, you might want to try hmCHIP, where you can obtain TFBS data for a set of intervals as in BED format.

ADD COMMENTlink written 8.2 years ago by Casey Bergman18k
gravatar for Gjain
8.0 years ago by
Göttingen, Germany
Gjain5.3k wrote:


if you go the ucsc test browser, there is more data available.

from there you can go to the UCSC table browser and in the group "regulation" you may find more tracks. Also, if you are working with HG19, then you can get hot spots and new peaks too.

Are you interested in tfbs from some specific lab or in general all the encode tfbs?

ADD COMMENTlink written 8.0 years ago by Gjain5.3k

At this point I am looking at all the encode tfs.

ADD REPLYlink written 7.9 years ago by Linda160
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