Download Transcription Factor Targeting Genes Data

Question

[I am]

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.

[Khader Shameer]

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

Answer 1

[Alex Reynolds]

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.).

[Raghav]

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

Answer 2

[Kamil]

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

It summarizes 6 datasets:

• TRED (2007)
• ITFP (2008)
• ENCODE (2012)
• Neph2012 (2012)
• TRRUST (2015)
• Marbach2016 (2016)

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.