I want to know which transcription factors bind to a specific region of the IL-10 promoter
Dear Jorge,
there are different approaches for answering your question:
a) the USCS browser contains tracks for a lot of more common transcription factors with easy to grasp graphics. Just browse for the gene of intrest in your specific organism and go to the region of interest.
b) Seqanswert has an open discussion about suitable databases. Unfortunately all of them rather start with a transcription factor of interest and then provide possible binding information
c) There are a lot of classical databases online that contain transcription factor binding motives. The most widely know is perhaps Transfac (registration needed, not free but I guess a free trial is possible). PROMO uses transfac data and provides links to alternatives. I would think that various alternatives exist of different quality.
best,
Andrea
https://genome.ucsc.edu/cgi-bin/hgGateway?redirect=manual&source=genome.ucsc.edu
http://seqanswers.com/forums/showthread.php?t=27484
http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3
There are several databases avaiable.....ALGGEN-PROMO, Tfsitescan, JASPAR, TFBIND, TESS, TRANSFAC......I have majorly used ALGGEN-PROMO
You can use footprintDB, is a compendium of TF motif databases, with different type of searches, one of them is when you write a consensus sequences and the program give you back which are the TFs that could bind to your interest sequence.
http://floresta.eead.csic.es/footprintdb/
Another possibility, but only works for Human sequences, is a website called Remap, where your input is a bed file with the coordinates of your sequences. The program give you back the name of the TFs that have ChIP-seq peaks (Public and Encode) overlapping your sequences.
http://tagc.univ-mrs.fr/remap/
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