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Nucleic Acids Res. 2015 Jan;43(Database issue):D97-102. doi: 10.1093/nar/gku1064. Epub 2014 Oct 31.

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

Author information

1
Institute of Bioinformatics, University Medical Center Göttingen, Georg August University, D-37077 Göttingen, Germany geneXplain GmbH, D-38302 Wolfenbüttel, Germany edgar.wingender@bioinf.med.uni-goettingen.de.
2
Institute of Bioinformatics, University Medical Center Göttingen, Georg August University, D-37077 Göttingen, Germany.
3
Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, Georg August University, D-37077 Göttingen, Germany.

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.

PMID:
25361979
PMCID:
PMC4383905
DOI:
10.1093/nar/gku1064
[Indexed for MEDLINE]
Free PMC Article

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