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?
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Nachocab •
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.
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.
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 ?
http://www.yeastract.com/ is good for Yeast transcription factors.
Another similar post . How To Identify Targets Of A Transcription Factor ?
If you are looking for plant transcription factors, you can try PlantRegMap.
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iRegulon Cytoscape app has an option by which we can identify the targets of a TF