The TFCat Project
The TFCat project was undertaken as a collaborative partnership between four groups:
- Timothy Hughes Lab, U. of Toronto
- Jared Roach Lab, Seattle Children’s Hospital Research Institute (work performed while at the Institute for Systems Biology)
- Rob Sladek Lab, McGill U.
- Wyeth Wasserman Lab, U. of British Columbia
The project was driven by Debra Fulton, the UBC graduate student who created the online resources, organized the annotation process, drafted the manuscript and implemented the classification system and homology-based candidate identification pipeline. The participating team included (in alphabetical order): Gwenael Bread, Debra Fulton, Tim Hughes, Jared Roach, Sarav Sundararajan, Rob Sladek and Wyeth Wasserman. In addition, a large number of individuals contributed expertise by reviewing the literature for annotation of protein function.
Origins Of The TF Collection
Each of the participating laboratories independently produced collections for their own use. As the groups had different purposes in their original efforts, we elected to take the union of the gene lists as input to a literature evidence-based pre-screening process to produce a list of TF gene candidates for curation. To ensure the comprehensiveness of our collection, we adopted an encompassing view of the meaning of “transcription factor”. However, most of the groups have specific interests in DNA-binding TFs and that may be apparent in the design and execution of the TFCat project. Over 2006-2007 we reviewed the literature for ~1000 candidate TFs and assigned functional properties from a controlled vocabulary (along with confidence levels). To assemble and order TFs with similar DNA-binding mechanisms, we incorporated and built upon a structural classification system (Luscombe et al.) for DNA binding proteins.
Debra L. Fulton, Saravanan Sundararajan, Gwenael Badis, Timothy R. Hughes, Wyeth.W. Wasserman and Jared C. Roach and Rob Sladek. TFCat: The curated catalog of mouse and human transcription factors. Genome Biology. 2009 Mar 12;10(3):R29.
Additional literature related to the development and use of TFCat is available on the TFCat Reference Page.