Question

Transcription Factors <--> Regulated Genes Database

4

Entering edit mode

11.2 years ago

enricoferrero ▴ 910

Hi,

I'm looking for a publicly accessible database that stores transcription factors to regulated genes relationships.

Ideally, I'm looking for something like:

TF1 geneX
TF1 geneY
TF1 geneZ
TF2 geneY
TF3 geneX
TF3 geneA
... ...

Is anything like that available?

Thanks!

database transcription-factor gene • 6.4k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 11.2 years ago by enricoferrero ▴ 910

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Have a look at this question: How to identify targets of a Transcription factor? http://pazar.info/ looks interesting, but I'm not sure that you can download the database.

An answer in that question also mentions: http://itfp.biosino.org/itfp/

ADD REPLY • link updated 4.9 years ago by Ram 44k • written 11.2 years ago by brentp 24k

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You might be interested in this paper: "Circuitry and dynamics of human transcription factor regulatory networks" by Stergachis and Neph, et al. http://www.ncbi.nlm.nih.gov/pubmed/22959076

ADD REPLY • link 11.2 years ago by Alex Reynolds 35k

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For what organism? Are you interested in all transcription factors, or only those thought to be expressed at a certain time point or in specific tissues? Or in one gene regulatory network? I am not aware of a tool that pools together all TF - target data. One thing you can do is script off of the GEO datasets -- if there are specific TF's you are interested in, someone may have made a mouse KO, studied gene expression, and the data will be posted to GEO. You can infer some targets that way. (But this will require some normalization statistics across experiments/platforms -- and it's still an inference.)

ADD REPLY • link 11.2 years ago by Alex Paciorkowski 3.5k

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yes, what an organism? If you are looking for bacterial transcription factors, there is a good database RegPrecise: http://regprecise.lbl.gov/RegPrecise/

ADD REPLY • link 11.0 years ago by khorms ▴ 230

Ram · Answer 1 · 2016-02-10

Hi enricoferrero,

I know this is a long halted question and a thread. However, I'm really interested to know whether you achieved what you wanted to achieve. If so, can you please share your ideas with us rest of stumblers upon the same question? Thanks a lot.

Shani.

P.S. I'm looking at the Arabidopsis TFs and their target genes. If anyone knows where to look, please guide me through. I already tried the AtRegNet, but still I'm not sure that is exactly what I want.