Question: Transcription Factors Used By Encode
2
gravatar for Larry_Parnell
7.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Does anyone know of a source listing all the human transcription factors currently under study or planned for study by ENCODE?

I know that for the small but growing number of TFs for which there are data the list can be pulled from the UCSC genome browser. I'd like to have the comprehensive list, something analogous to that from FANTOM (Ravasi 2010 Cell 140: 744-752).

transcription-factor encode • 3.1k views
ADD COMMENTlink written 7.7 years ago by Larry_Parnell16k
1

Hi! Is this is what you are looking for?

ADD REPLYlink written 7.7 years ago by Vikas Bansal2.4k

Not exactly what I would like (the table, although extensive, only lists data available and not those ChIP-Seq expts that are planned), but extracting the ChIP-Seq rows will give me useful info on which TFs ENCODE has examined.

ADD REPLYlink written 7.7 years ago by Larry_Parnell16k

The encoce wiki has all the list of the factors (100+) but I think you have to have an account on that.

here is the link http://encodewiki.ucsc.edu/EncodeDCC/index.php/Main_Page

ADD REPLYlink modified 7.7 years ago • written 7.7 years ago by Gjain5.4k
1
gravatar for Gjain
7.7 years ago by
Gjain5.4k
Munich, Germany
Gjain5.4k wrote:

Hi Larry,

If you can access this page here is a comprehensive list.

http://encodewiki.ucsc.edu/EncodeDCC/index.php/ENCODE_Data_Analysis_Center_%28DAC%29

ADD COMMENTlink written 7.7 years ago by Gjain5.4k

That page is password protected. So, unless you are a member of the project team, accessing the list of TFs is difficult.

ADD REPLYlink written 7.7 years ago by Larry_Parnell16k
1
gravatar for Mary
7.7 years ago by
Mary11k
Boston MA area
Mary11k wrote:

This page at the ENCODE has the registered antibodies: http://genome.ucsc.edu/ENCODE/antibodies.html

But I don't know if that includes intended ones. Some time ago one of the labs ran a page to let you nominate TFs of interest that they could investigate, but that page is now dead. I'll see if I can get someone associated with the project to come by.

ADD COMMENTlink written 7.7 years ago by Mary11k
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