transcription factor database

[Tonino]

Hi,
Is there a database that tells you which transcription factor influences a gene?

For example, if I wanted to know which TF influenced GFP15, is there a database that could quickly whip up this information?

Thank you.
Bryan.

[morkfromork]

It's pretty difficult to predict targets of transcription factors or to predict what TFs might regulate a gene without doing an actual experiment. You can of course look for TF binding sites in the promoter, but in my experience (with mammalian genes) you will probably find sites for absolutely everything. With something like yeast where regulatory regions are a little more compact you might have a chance to predict just by looking at sequences.

[memari]

http://www.sabiosciences.com/chipqpcrsearch.php


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BABAK
https://babakmemari.wordpress.com

[ProteinLounge]

ProteinLounge has a transcription factor database: http://www.proteinlounge.com/Database/Databases.aspx.

[mdfenko]

ProteinLounge has a transcription factor database: http://www.proteinlounge.com/Database/Databases.aspx.

this is a paid subscription service

[morkfromork]

Hi,
Is there a database that tells you which transcription factor influences a gene?

For example, if I wanted to know which TF influenced GFP15, is there a database that could quickly whip up this information?

Thank you.
Bryan.

In some organisms there are ChIP-seq data available (i.e.through UCSC genome browser). These might tell you if a TF is binding to your gene of interest, but it does not necessarily mean the TF regulates that gene (many TF binding sites are not functional regulatory elements).

Predicting TFs that regulate a gene de novo is pretty much impossible and I would be very skeptical of anyone saying they could do this for large genomes such as human and mouse. I certainly wouldn't pay for access to a database of predicted TF sites. Finding motifs is pretty much worthless, you will usually find binding sites for every TF under the sun if you search a gene promoter.

Another thing you might try is to look through microarray data of TF knockouts and see if any of them alter expression of your gene.