Question: How To Identify Targets Of A Transcription Factor ?
16
gravatar for Khader Shameer
7.3 years ago by
Manhattan, NY
Khader Shameer17k wrote:

I have a list of transcription factors from a high-throughput experiment. I would like to know about the probable target genes of these transcription factors. For example using OregAnno, I found that target gene of KLF6 is LTC4S. OregAnno seems to be not up-to-date. Is there any other bioinformatics resource where I can find the human TF->Target information ?

transcription • 19k views
ADD COMMENTlink modified 2.1 years ago by nivi19720 • written 7.3 years ago by Khader Shameer17k
1

i think by reverse engineering tools such as ARACNe you can define Targets Of A Transcription Factor

ADD REPLYlink written 2.3 years ago by Fereshteh2.8k
6
gravatar for Larry_Parnell
7.3 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Tough question. Most people want to go from gene to TF regulating that gene instead of TF to all genes under its (partial) control. What also makes this tough are: 1) tissue-specificity, 2) predictions of one or few binding sites when in vitro/in vivo data would suggest that the particular TF needs to bind multiple times, typically in cooperative fashion, in order to promote transcription. Other complications are different mRNA isoforms under control of different, perhaps overlapping TFs and genome variation altering regulation by a particular TF.

I know that none of this points you to a database of TF-gene interactions. I know of none that would address the above points - and those are relevant to the way I look at this question.

ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by Larry_Parnell16k
1

I don't know but I doubt they consider these items. The real deep detailed stuff I have seen puts focus on just one TF. But one of ~2000 certainly won't cut it for your work.

ADD REPLYlink written 7.3 years ago by Larry_Parnell16k

Larry: Thanks for your suggestions on why this is difficult. I am wondering whether or OregAnno or other database that reports target information consider these important aspects.

ADD REPLYlink written 7.3 years ago by Khader Shameer17k

Thanks for your suggestions.

ADD REPLYlink written 7.3 years ago by Khader Shameer17k
5
gravatar for Mikael Huss
7.3 years ago by
Mikael Huss4.5k
Stockholm
Mikael Huss4.5k wrote:

You could try http://pazar.info/ and http://itfp.biosino.org/itfp/ for starters.

ADD COMMENTlink written 7.3 years ago by Mikael Huss4.5k
1

This new paper describes another database server which might fit the bill (haven't checked it yet): http://www.ncbi.nlm.nih.gov/pubmed/20709693?dopt=Abstract

ADD REPLYlink written 7.3 years ago by Mikael Huss4.5k

I will check these resources and get back to you.

ADD REPLYlink written 7.3 years ago by Khader Shameer17k
5
gravatar for Khader Shameer
6.6 years ago by
Manhattan, NY
Khader Shameer17k wrote:

I recently used "Investigate Gene Sets" options in MSigDB to find the transcription factor target information of my dataset. Adding this here as an answer for future googlers.

The data is curated from TRANSFAC, you can do a 'Compute Overlap' of your genes with the list of genes in the dataset. Output includes a p-value to indicate statistical significance and a Gene/geneset overlap matrix to visualize the gene categorized into different transcription factor targets.

Data set is available here.

ADD COMMENTlink written 6.6 years ago by Khader Shameer17k
1

Looks like a good resource! Thanks!

ADD REPLYlink written 6.4 years ago by Kate370
4
gravatar for Travis
4.0 years ago by
Travis2.7k
USA
Travis2.7k wrote:

Old question but still relevant and think this resource answers it:

http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchTFGeneForm

ADD COMMENTlink written 4.0 years ago by Travis2.7k

@Travis, I think so too, except I have not gotten it to work yet.

ADD REPLYlink written 17 months ago by a.aiezza30
2
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
1
gravatar for Dejian
6.9 years ago by
Dejian1.2k
United States
Dejian1.2k wrote:

I agree with Larray on that people usually try to search for TFs acting on the interested genes. I have two suggesions to solve this problem. First, we can do it as usual, or find the TFs for all the genes in the genome (if available) of your research species and then select those genes posessing your TFs.This poissibly will take much time for computation. Furthermore, this probably has been done for model organisms and relavant databases may be available.Replicate the procedure and apply it to your own species.MAPPER can help do this. Second, try to find some ChIP data about your TF.If you are lucky and such kind of data is available,it will be a great help.The two suggestions may turn out to be useless since they are based on some preconditions that may be unavailable.

ADD COMMENTlink written 6.9 years ago by Dejian1.2k

Thanks Balance.

ADD REPLYlink written 6.9 years ago by Khader Shameer17k
1
gravatar for Michael Dondrup
6.9 years ago by
Bergen, Norway
Michael Dondrup43k wrote:

There is also the Transfac database which is a commercial database of TF and interactions with subscription (now, I thought they had had a free portion before?).

As a wet-lab approach the exact solution to your question would be ChIP-sequencing (or ChIP-chips).

ADD COMMENTlink written 6.9 years ago by Michael Dondrup43k

Michael, Thanks,

ADD REPLYlink written 6.9 years ago by Khader Shameer17k
1
gravatar for Gurado
6.6 years ago by
Gurado280
Gurado280 wrote:

If you are happy to go with predictions have a look at the MEME suite http://meme.sdsc.edu/ Just be aware that you are getting plenty of false positives. To get a more accurate picture for a particular scenario have a go with ChipSeq.

ADD COMMENTlink written 6.6 years ago by Gurado280
0
gravatar for nivi1972
2.1 years ago by
nivi19720
United States
nivi19720 wrote:

I am working in the same.I have a list of Transcription factors, their target genes and miRNAs all involved in skin cancer. Actually i want to make a directed regulatory network. But the problem is how to make it direct because all the databases mentioned above not provide information about what kind of regulation exist? weather it is activation or inhibition or coactivation like that. Manual annotation seems very difficult for me as i have huge data. Please suggest any database, plugins or method so that i can get such type of regulatory information. 

Thanks

ADD COMMENTlink written 2.1 years ago by nivi19720

SIREN package by can identify activation or inhibition type of regulation

http://baderlab.org/PegahKhosravi/SIREN

ADD REPLYlink written 2.1 years ago by Fereshteh2.8k
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