Abstract
TFClass is a resource that classifies eukaryotic transcription factors (TFs) according to their DNA-binding domains (DBDs), available online at http://tfclass.bioinf.med.uni-goettingen.de. The classification scheme of TFClass was originally derived for human TFs and is expanded here to the whole taxonomic class of mammalia. Combining information from different resources, checking manually the retrieved mammalian TFs sequences and applying extensive phylogenetic analyses, >39 000 TFs from up to 41 mammalian species were assigned to the Superclasses, Classes, Families and Subfamilies of TFClass. As a result, TFClass now provides the corresponding sequence collection in FASTA format, sequence logos and phylogenetic trees at different classification levels, predicted TF binding sites for human, mouse, dog and cow genomes as well as links to several external databases. In particular, all those TFs that are also documented in the TRANSFAC® database (FACTOR table) have been linked and can be freely accessed. TRANSFAC® FACTOR can also be queried through an own search interface.
Highlights
Transcription factors (TFs) are proteins that regulate transcription, e.g. by directing RNA polymerase to the transcription start site of a gene
Most TFs do so by recognizing regulatory elements in promoters and enhancers in a sequence-specific way through their DNA-binding domains (DBDs). These DBDs are organized by few structural principles, which can be used to classify DNA-binding TFs as we have done with TFClass
We present the extension of TFClass to all mammals as far as annotated genomic information is available
Summary
Transcription factors (TFs) are proteins that regulate transcription, e.g. by directing RNA polymerase to the transcription start site of a gene. The TFs assigned in TFClass are linked to entries in the FACTOR table of the TRANSFAC® database, the oldest actively maintained resource for TFs and their DNA-binding sites and properties (4). Using the catalog of human TFs from previous versions of TFClass as starting point, we retrieved the corresponding ortholog clusters from OrthoDB.
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