Need Information About Human Tfs Indentified By The Encode Project

Question

[nazaninhoseinkhan]

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.

Regards

Nazanin

[Devon Ryan]

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

Answer 1

[Charles Warden]

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:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=362498299&c=chr17&g=wgEncodeReg

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):

https://genome.ucsc.edu/ENCODE/

http://www.genome.gov/10005107

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:

http://funseq.gersteinlab.org/

Answer 2

[PoGibas]

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.