TFClass: a classification of human transcription factors and their rodent orthologs

Abstract

TFClass aims at classifying eukaryotic transcription factors (TFs) according to their DNA-binding domains (DBDs). For this, a classification schema comprising four generic levels (superclass, class, family and subfamily) was defined that could accommodate all known DNA-binding human TFs. They were assigned to their (sub-)families as instances at two different levels, the corresponding TF genes and individual gene products (protein isoforms). In the present version, all mouse and rat orthologs have been linked to the human TFs, and the mouse orthologs have been arranged in an independent ontology. Many TFs were assigned with typical DNA-binding patterns and positional weight matrices derived from high-throughput in-vitro binding studies. Predicted TF binding sites from human gene upstream sequences are now also attached to each human TF whenever a PWM was available for this factor or one of his paralogs. TFClass is freely available at http://tfclass.bioinf.med.uni-goettingen.de/ through a web interface and for download in OBO format.

Figure 1.

Superclass distribution of human TF genes and their mouse orthologs.

Figure 2.

Web interface of human and mouse TFClass. In the center, the classification of human TFs is shown by default, on the right is the classification of mouse TFs. Navigating to a certain entity in the human classification (here: c-Myc) automatically opens the mouse classification to the same point. Note that the subfamily displayed here contains one human-specific factor (L-Myc-2, 1.2.6.5.4) in the central part and one mouse-specific TF (B-Myc, 1.2.6.5.6) on the right-hand side. On the left, additional information for the selected human TF is given, including external database links. The button ‘Switch classifications’ on top allows the user to put the mouse classification as primary one in the center, which would also switch the additional information on the left from human to mouse.