Question: Download Transcription Factor Targeting Genes Data
1
gravatar for I am
5.1 years ago by
I am60
United States
I am60 wrote:

Hello all,

I want to create human transcriptional regulatory network. Can someone tell me an updated database, which can tell me transcription factors targeting genes?

Thanks in advance.

transcription • 2.9k views
ADD COMMENTlink modified 13 months ago by Kamil1.7k • written 5.1 years ago by I am60

See highly related post on same topic here: http://biostars.org/post/show/2148/

ADD REPLYlink written 5.1 years ago by Khader Shameer17k
5
gravatar for Alex Reynolds
5.1 years ago by
Alex Reynolds21k
Seattle, WA USA
Alex Reynolds21k wrote:

We very recently published a paper in *Cell* which looks at TF regulatory networks in human. In addition to procedural and reference material that might help you out, data downloads are available through Cell's site, and I put together a web application that allows exploring interactions in a variety of cell types.

We also have PWMs available for discovered motifs. You could run these through a tool like TOMTOM to find TF matches across other databases (TRANSFAC, JASPAR, etc.).

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Alex Reynolds21k

Dear Sir, it is very informative article regarding TF regulatory network, I tried to download complete network but due to inaccessibility of journal I am unable to get the complete Network. It is my kind request to provide me complete Tf regulatory network

ADD REPLYlink written 4.3 years ago by Raghav100
1
gravatar for Kamil
13 months ago by
Kamil1.7k
Boston
Kamil1.7k wrote:

You might be interested in this R package: https://github.com/slowkow/tftargets

It summarizes 6 datasets:

See make_rdata.R for the script that converts the raw data into lists of gene sets.

Usage Example

  • Show the names of the lists.
  • Show the names of the first 5 transcription factors in TRRUST.
  • Show the gene targets for the AIP transcription factor.

screenshot

ADD COMMENTlink written 13 months ago by Kamil1.7k
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