Target Promoters Of A Transcription Factor

Question

[Reyhaneh]

how can I figure out what are the promoters that a transcription factor attaches to them? I want experimental information. is there any site?

Answer 1

[seidel]

Your question is fairly unclear given that there are many more transcription factors known than there are binding sites to go along with them, and any given factor for which a site is known typically binds a variety of sites. Two of the most popular databases of factors and sites are TRANSFAC and Jaspar. The sites are based on experimental information. Your question about promoters is also vague. What counts as the promoter? What organism? Most people would have to isolate a set of promoters under a given set of criteria, and then assess in silico whether those promoters contain sites of interest (as described by a position specific weight matrix), or they would do a real experiment for a given factor and measure something in the lab (which do you mean?).

There are databases based on experimental evidence of various kinds, such as:

http://www.flyreg.org/ and http://rulai.cshl.edu/cshlmpd/ etc.

There is also the literature, depending on your interest. Several papers describe genome-wide binding of a given transcription factor under a set of conditions, and the associated data is available. See for example the Pho4 study of Zhou and O'Shea 2011 http://www.ncbi.nlm.nih.gov/pubmed/21700227

try googling: transcription factor promoter database, and you'll find a trail to follow.

Answer 2

[Asaf]

If you're interested in human, you should check out the integrated regulation track from ENCODE in the UCSC genome browser, you can see (and download data for) binding sites of various TF in several cell lines.

Answer 3

[Paul Denny]

Another alternative source is the ENSEMBL genome browser

which also presents the ENCODE experimental regulatory data for TF binding sites from mouse, human and other species from various sources e.g. cell lines.

Answer 4

[Reyhaneh]

Thanks for all answers.

But I mean for example:

I want to know transcription Factor X binds to which genes. I need these genes in order to design Primers to test them by qPCR.

[Ying W]

please edit your original question and add this in. the only way to know if the TF of interest binds to a gene is to use an experimental technique such as Chromatin immunoprecipitation (ChIP). You can also look on UCSC genome browser and hope that ENCODE has done ChIP-seq (genome wide ChIP) on the TF you are interested in, if not you would have to either look in literature to see if someone has done ChIP-seq for your protein/cell line or you would have to find antibodies and do it yourself