How To Get A List Of Genes Regulated By A Transcription Factor?
5
2
Entering edit mode
12.4 years ago
Nachocab ▴ 100

I'm looking for a database that has a list of the predicted genes that have a binding site in their promotor region for a given transcription factor. Something like this: http://www.sabiosciences.com/chipqpcrsearch.php?gene=&species_id=0&factor=NF-kappaB&ninfo=n&ngene=y&nfactor=n but they don't have any sources, so I can't figure out where they get this information or what their algorithm does.

Any ideas?

transcription-factor • 4.7k views
ADD COMMENT
1
Entering edit mode

iRegulon Cytoscape app has an option by which we can identify the targets of a TF

ADD REPLY
3
Entering edit mode
12.4 years ago

One option is ORegAnno. You can search there for a specific gene of interest. Or download the whole dataset (use the tab-delim files which are most complete). Or, browse through the list of TFs by species and gets lists of target genes for each using the TfView tool. Other good options are Pazar and TFCat which can also be browsed by TF. Also, see this related question.

ADD COMMENT
2
Entering edit mode
12.4 years ago
raunakms ★ 1.1k

If you are looking for prokaryotic transcription factors then PRODORIC (http://prodoric.tu-bs.de/) is the best resource for the purpose you have mentioned.

ADD COMMENT
0
Entering edit mode

I'm actually interested in eukaryotes, but in your site, how do I get to a list of genes from a TF like this one: http://prodoric.tu-bs.de/site.php?site_acc=SI000652 ?

ADD REPLY
1
Entering edit mode
12.4 years ago

http://www.yeastract.com/ is good for Yeast transcription factors.

ADD COMMENT
1
Entering edit mode
8.1 years ago
Ron ★ 1.2k

Another similar post . How To Identify Targets Of A Transcription Factor ?

ADD COMMENT
0
Entering edit mode
8.1 years ago
jin ▴ 80

If you are looking for plant transcription factors, you can try PlantRegMap.

ADD COMMENT

Login before adding your answer.

Traffic: 1996 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6