Transcription factor databases

The following is a guest-post by my colleague Jacqueline Lane (with some editing by me). She has been interested in identifying novel transcription factors (TF) involved in obesity and genetic variants in their binding sites as well as in the TF genes themselves.

Jackie has put together a list of TF-gene interaction databases she is willing to share here. There are three types of data:

1) TF-gene interaction
This is a compilation of databases with TF-gene interaction data. This might be of the most interest because it lists many databases. See http://www.pazar.info/. There is also the oRegAnno database, which is easy to view if you click on the tfview link on the right-hand side; see http://www.oreganno.org/oregano/. Lastly, TF-gene binding data can also be found at http://www.tfcat.ca/.

2) TF-TF interactions
This is a database of TF-TF co-activators and co-repressors (TFs that direct transcription of a gene in concert). This helps with determining tissue/temporal specific combinatorial regulation. See http://www.cell.com/retrieve/pii/S0092867410000796.

3) TF co-activators
The TF co-factor database lists proteins that bind to TFs, but not directly to DNA. These protein interactions can give a better picture of the full interaction. Find the data at http://nar.oxfordjournals.org/content/early/2010/10/20/nar.gkq945.full.