Question: How Can I Find Target Genes Of A Transcription Factor?
3
gravatar for Reyhan
5.7 years ago by
Reyhan30
Reyhan30 wrote:

how can I find target genes of a transcription factor?

gene target transcription • 12k views
ADD COMMENTlink modified 13 months ago by jin80 • written 5.7 years ago by Reyhan30

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.

ADD REPLYlink written 5.7 years ago by Neilfws47k
4
gravatar for 2184687-1231-83-
5.7 years ago by
2184687-1231-83-4.8k wrote:

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

ADD COMMENTlink written 5.7 years ago by 2184687-1231-83-4.8k

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

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Kamil1.7k

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

ADD REPLYlink written 2.7 years ago by Ashutosh Pandey11k
3
gravatar for Ericc
5.7 years ago by
Ericc50
Ericc50 wrote:

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.

ADD COMMENTlink written 5.7 years ago by Ericc50
2
gravatar for Sean Davis
5.7 years ago by
Sean Davis23k
National Institutes of Health, Bethesda, MD
Sean Davis23k wrote:

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

ADD COMMENTlink written 5.7 years ago by Sean Davis23k
1
gravatar for Obi Griffith
5.7 years ago by
Obi Griffith16k
Washington University, St Louis, USA
Obi Griffith16k wrote:

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.

ADD COMMENTlink written 5.7 years ago by Obi Griffith16k
1
gravatar for Kamil
2.7 years 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 modified 13 months ago • written 2.7 years ago by Kamil1.7k
0
gravatar for Ryan Dale
5.7 years ago by
Ryan Dale4.6k
Bethesda, MD
Ryan Dale4.6k wrote:

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

ADD COMMENTlink written 5.7 years ago by Ryan Dale4.6k
0
gravatar for jin
13 months ago by
jin80
jin80 wrote:

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

ADD COMMENTlink written 13 months ago by jin80
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