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. 2018 Jan 4;46(D1):D343-D347.
doi: 10.1093/nar/gkx987.

TFClass: Expanding the Classification of Human Transcription Factors to Their Mammalian Orthologs

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Free PMC article

TFClass: Expanding the Classification of Human Transcription Factors to Their Mammalian Orthologs

Edgar Wingender et al. Nucleic Acids Res. .
Free PMC article

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.

Figures

Figure 1.
Figure 1.
Screenshot of a Family page (A) and a Genus list (B) in TFClass. (A) The example shows the page for family 2.1.3, RXR-related nuclear receptors with some summarizing information in the upper and thumbnails of the phylogenetic trees in the lower part. Here, the upper four trees refer to all TFs of this family, whereas the lower four trees show the relations between the corresponding TFs from human, mouse, cow and Monodelphis only (‘slim selection’). (B) The insert shows the beginning of the list of species-specific instances for RXRalpha (2.1.3.1.1), with human and mouse entries put at the top of the list. The top yellow bar on the right of each entry represents the ‘canonical’ form of the corresponding UniProt entry. For the splice variants underneath, those parts of the molecule that diverge from the canonical form are highlighted by light-grey areas, the position of the DBD is indicated by the dark-grey box behind the bars.

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References

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