Click here to go straight to the classification of human transcription factors.
September 22, 2014: The classification of murine TFs that have human orthologs has been finalized, including UniProt and TRANSFAC® links. It documents 1147 TF genes, enconding more than 1780 proteins.
July 27, 2014: For all human TFs including numerous new splice variants, the links to TRANSFAC and Protein Atlas have been updated.
July 26, 2014: For most human TFs (up to family 5.3.4), the links to TRANSFAC and Protein Atlas have been updated.
July 14, 2014: For all human TF genes ("genus" level of the classification with five-digit classification numbers), mouse and rat orthologs were added. They were mainly retrieved from UniProt, manually double-checked for by human-mouse-rat alignments and occasionally identified or confirmed by additional BLAST searches.
February 23, 2013: Many transcription factors were linked to logo plots describing their DNA-binding specificity. They were constructed by Philip Stegmaier (my special thanks to him!) on the basis of the Positional Weight Matrix library recently published by the group of Jussi Taipale (Jolma et al., Cell 152, 327-339 (2013); PubMed 23332764).
November 17, 2012: Links to the RCSB Protein Data Bank (PDB) were included, referring to 3D structures of DNA-binding domain (DBD)/DNA complexes, provisionally the DBD alone. One illustrative example has been selected in cases where several PDB entries are available.
August 26, 2012: Additional information about the DNA-binding domains constituting a Class, their alignments and further details have been linked to each Class entry. A number of duplicates and other errors were erased (special thanks to Torsten in Göttingen and Tagir in Novosibirsk for their hints!). Database links were completely revised according to UniProt version 2012_07 and TRANSFAC release 2012.2.
March 10, 2012: for this version, the bZIP factors class (1.1) has been subjected to major revision, due to extensive phylogenetic analyses and some additional considerations of molecular properties of bZIP factors (e.g., amino acid residues in positions known to be essential for DNA contacts, dimerization behavior, visual inspection of group consensi and of the subdomains such as basic, linker, and ziper region). Some re-arrangements have been introduced to the homeo domain class (3.1) and some others. Attempts were made to unify the nomenclature further (e.g., "x-related factors" for family, "x-like factors" for subfamilies). Exemplary DNA sequences known to interact with at least some of the factors of a certain taxon have been introduced for many families or subfamilies.
November 27, 2011: The classification is now complemented with links to TRANSFAC Professional throughout (thanks to the colleagues from BIOBASE for their help). At this opportunty, a number of minor mistakes were corrected.
October 29, 2011: Seven DUX4-like proteins were introduced into subfamily 126.96.36.199. A new class of an yet undefined DNA-binding domain was documented as 0.4 Class: NFX1-type putative zinc fingers, and the transient class of uncharacterized DNA-binding domains (0.0) was enriched by the tentative families PHF5 (0.0.2), RFXANK (0.0.3), and RFXAP (0.0.4). A series of numbering issues were corrected after they were brought to my attention; my thanks to Tagir in Novosibirsk!
October 14, 2011: Four new classes were introduced in superclass 2 (zinc-coordinating DNA-binding domains): 2.6: CXXC zinc fingers; 2.7: C2HC zinc fingers; 2.8: C3H zinc fingers; 2.9: C2CH THAP-type zinc fingers. In addition, a superclass "0" was appended to group classes of DNA-binding factors the DNA-binding domain of which has not been structurally characterized. So far, four classes comprising 9 TF (genes) have been assigned to this transient superclass.
September 18, 2011: All classes and superclasses have been linked to a class description, taken in most cases from the TRANSFAC database, but complemented by new descriptions where necessary. New: 3.7 Class: ARID.
June 19, 2011: A first draft for a classification of 711 C2H2 zinc finger factors has been introduced (Class 2.3); due to its preliminary character, the numbering scheme should be taken as tentative!
June 19, 2011: Family 3.5.1 has been re-worked: It has been re-named to "Myb-/SANT-domain factors", with altogether 7 sub-families. Two new subfamilies have been introduced in the Class 1.2 (bHLH): 188.8.131.52 Subfamily: bHLHa9 (to 1.2.3, Family "Tal/Twist/Atonal/Hen") and 184.108.40.206 Subfamily: SOHLH-like factors (to 1.2.5, Family "PAS domain factors"). Factor FIGalpha (220.127.116.11.8), Mesogenin (18.104.22.168.6) and Mnt (22.214.171.124.6 ) have been newly assigned.
March 21, 2011: Three new classes were included: Class 2.5: Intertwined zinc fingers of DM (doublesex & mab-3) type (previous Class 2.5 "Zinc fingers of alternating composition" has been re-numbered to Class 2.6); Class 6.6: NDT80; Class 7.2: GCM.
March 13, 2011: Those TF covered by the classification have been linked to the Human Protein Atlas from Uppsala University & KTH.