How Can I Find Target Genes Of A Transcription Factor?

Question

[Reyhan]

how can I find target genes of a transcription factor?

[Neilfws]

I'm deleting your second question from the answers section. Please use the comments underneath answers for further questions, rather than posting a question as an answer.

Answer 1

[2184687-1231-83-]

If you have ChIP-seq data, you can use TIP:
http://bioinformatics.oxfordjournals.org/content/27/23/3221

[Kamil]

Can you provide a link to download the TIP software? There is no link in the paper or on Mark Gerstein's lab website.

[Ashutosh Pandey]

Here you go: http://archive.gersteinlab.org/proj/tftarget/

Answer 2

[Ericc]

I think there are two ways to do this: 1. You can check the ChIP-chip and ChIP-Seq data from GEO and ENCODE for your TF. This is the direct evidence that the TF binds to the targets. But the TF binding is a dynamic/tissue specific process, so make sure the ChIP-chip and ChIP-Seq experiment performed in the similar tissue/cell type you are interested in. 2. Or if you know the motif of that TF (check Transfac), you can use the motif to scan the gene promoters. If the promoter contain the motif (usually this region should also be conserves across multiple species), then the corresponding gene might be the target of that TF. This is just a computational prediction.

Answer 3

[Sean Davis]

You might check MSigDB. Also, the ENCODE project has an ever-expanding list of ChIP-Seq datasets that might be relevant.

Answer 4

[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.

Answer 5

[Obi Griffith]

Check out PAZAR. They have a downloads page with TFs and the genes regulated by them. This is a curated set built from the literature, other databases (e.g., ORegAnno), ChIP-Seq datasets, and more.

Answer 6

[Ryan Dale]

TIP is mentioned in another answer; another algorithm to try is EMBER (Expectation Maximization of Binding and Expression pRofiles).

Answer 7

[jin]

For target genes of plant transcription factors, you can find it in PlantRegMap