Question: Need Information About Human Tfs Indentified By The Encode Project
gravatar for nazaninhoseinkhan
5.1 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan360 wrote:

Hello everybody,

I want to know if all binding sites of identified human transcription factors have been specified in ENCODE project? Or, are there some TFs that no binding sites have been specified for them.



transcription-factor encode • 1.3k views
ADD COMMENTlink modified 5.1 years ago by SES8.1k • written 5.1 years ago by nazaninhoseinkhan360

1) No they have not. 2) Probably. I'm sure there's some obscure enhancer element with known effector genes but unknown binding properties.

ADD REPLYlink written 5.1 years ago by Devon Ryan88k
gravatar for Charles Warden
5.1 years ago by
Charles Warden6.4k
Duarte, CA
Charles Warden6.4k wrote:

I'm not sure what is the best fit for the specific data you need to analyze.

I think a generally good place to start would be the ENCODE tracks on the UCSC Genome Browser. When you zoom in, you can see the binding sites for specific transcription factors. So, I assume you could parse the table to determine the list of all tested TFs, the genomic range they cover, etc:

Also, it looks like the 2012 freeze even tells you that there were 161 targets and 189 antibodies. For basic stats like that, I would image you could also get them from the ENCODE website(s):

Finally, different tools may be better suited for different goals. For example, using a tool like FunSeq (which includes ENCODE annotations) may be the most efficient way to annotate non-coding variants in a .vcf file:

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Charles Warden6.4k
gravatar for PoGibas
5.1 years ago by
PoGibas4.7k wrote:

I don't know what you mean by "specified", but in this article (main ENCODE paper on TFs) they write about novel identified motifs.
See section "Footprints encode an expansive cis-regulatory lexicon" -- they identified 289 novel motifs (by novel they mean "doesn't match any entry in main TF databases").

PS.: Change question title to a more informative more.

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by PoGibas4.7k
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