Transcription Factor Classification

This project is dedicated to continuous updating of a previous classification of eukaryotic transcription factors (TFs) according to their DNA-binding domains (1-3). The present classification focuses on human TFs (3), has later been extended to rodents (mouse and rat) (2), and has been applied recently to al mammalian taxa (1). The aim of this classification is to provide a basis for deciphering the protein-DNA recognition code. That would lead to a comprehensive understanding of how the read-out of regulatory information encoded in the genome by proteins works.

By inspection of structural and sequence similarities of the proteins that are known or can be reasonably assumed to act as TFs, a six-level classification scheme was created to which altogether more than 1500 human TFs genes, coding for more than 2900 proteins, can be assigned. They were grouped into 111 families, many of them divided into subfamilies. They constitute 40 classes and 9 superclasses (formerly only 4). Further details are given in Refs. 4-6.

The access to the classification has been organized by J. Dönitz' OBA server (7). The project page can be found here:

http://tfclass.sybig.de

The most recent draft version of the human TF classification can be found as flat html document on Prof. E. Wingender's personal home page:

http://www.edgar-wingender.de/huTF_classification.html

and for mouse orthologs:

http://www.edgar-wingender.de/muTF_classification-1.html


Publications:

  1. Wingender,E., Schoeps,T., Haubrock,M., Krull,M. and Dönitz,J. (2017) TFClass: expanding the classification of human transcription factors to their mammalian orthologs. Online publication Nucleic Acids Res. 2017, doi: 10.1093/nar/gkx987.
  2. Wingender,E., Schoeps,T., Haubrock, M. and Dönitz,J. (2015) TFClass: a classification of human transcription factors and their rodent orthologs. Nucleic Acids Res., 43, D97-D102. Online publication Nucleic Acids Res. 2014, doi: 10.1093/nar/gku1064.
  3. Wingender,E., Schoeps,T. and Dönitz,J. (2013) TFClass: An expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41, D165-D170 (2013) Online publication Nucleic Acids Res. 2012, doi: 10.1093/nar/gks1123.
  4. Wingender,E. (2013) Criteria for an updated classification of human transcription factor DNA-binding domains. J. Bioinform. Comput. Biol., 11, 1340007.
  5. Heinemeyer,T., Chen,X., Karas,H., Kel,A.E., Kel,O.V., Liebich,I., Meinhardt,T., Reuter,I., Schacherer,F. and Wingender,E. (1999) Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res., 27, 318-322.
  6. Wingender,E. (1997) Classification of eukaryotic transcription factors. Mol. Biol. Engl. Tr., 31, 483-497.
  7. Dönitz,J. and Wingender,E. (2012) The ontology-based answers (OBA) service: A connector for embedded usage of ontologies in applications. Front. Gene., 3, 197.