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Database Commons - TFClass

TFClass

Citations: 48

z-index 6.05

Short name TFClass
Full name Classification of Human Transcription Factors and Mouse Orthologs
Description TFClass is a classification of human transcription factors (TFs) and their mouse orthologs based on the characteristics of their DNA-binding domains.
URL http://tfclass.bioinf.med.uni-goettingen.de/tfclass
Year founded 2012
Last update & version 2014-10-31    v2.0
Availability Free to all users
University/Institution hosted Georg August University
Address D-37077 Göttingen
City Göttingen
Province/State
Country/Region Germany
Contact name Edgar Wingender
Contact email edgar.wingender@bioinf.med.uni-goettingen.de
Data type(s)
Major organism(s)
Keyword(s)
  • dna-binding domain
  • mouse ortholog
  • transcription factor
Publication(s)
  • TFClass: a classification of human transcription factors and their rodent orthologs. [PMID: 25361979]

    Edgar Wingender, Torsten Schoeps, Martin Haubrock, Jürgen Dönitz
    Nucleic acids research 2015:43(Database issue)
    6 Citations (Google Scholar as of 2015-12-25)

    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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • TFClass: an expandable hierarchical classification of human transcription factors. [PMID: 23180794]

    Edgar Wingender, Torsten Schoeps, Jürgen Dönitz
    Nucleic acids research 2013:41(Database issue)
    42 Citations (Google Scholar as of 2016-04-25)

    Abstract: TFClass (http://tfclass.bioinf.med.uni-goettingen.de/) provides a comprehensive classification of human transcription factors based on their DNA-binding domains. Transcription factors constitute a large functional family of proteins directly regulating the activity of genes. Most of them are sequence-specific DNA-binding proteins, thus reading out the information encoded in cis-regulatory DNA elements of promoters, enhancers and other regulatory regions of a genome. TFClass is a database that classifies human transcription factors by a six-level classification schema, four of which are abstractions according to different criteria, while the fifth level represents TF genes and the sixth individual gene products. Altogether, nine superclasses have been identified, comprising 40 classes and 111 families. Counted by genes, 1558 human TFs have been classified so far or >2900 different TFs when including their isoforms generated by alternative splicing or protein processing events. With this classification, we hope to provide a basis for deciphering protein-DNA recognition codes; moreover, it can be used for constructing expanded transcriptional networks by inferring additional TF-target gene relations.

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200 OK2017-02-03
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200 OK2017-01-20
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200 OK2016-10-14
200 OK2016-10-11
200 OK2016-10-07
200 OK2016-10-04
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200 OK2016-07-15
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200 OK2016-07-08
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200 OK2016-06-17
200 OK2016-06-14
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200 OK2016-05-24
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200 OK2016-04-19
200 OK2016-04-15
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200 OK2016-04-08
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200 OK2016-03-29
200 OK2016-03-28
200 OK2016-03-25
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200 OK2016-03-21
200 OK2016-03-18
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200 OK2016-03-14
200 OK2016-03-11
200 OK2016-03-09
200 OK2016-03-07
200 OK2016-03-04
200 OK2016-03-02
200 OK2016-02-29
200 OK2016-02-26
200 OK2016-02-24
200 OK2016-02-22
200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
200 OK2016-02-12
200 OK2016-02-10
200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

Protein
Homo sapiens Mus musculus
dna-binding domain mouse ortholog transcription factor

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lina Ma [2016-09-26]
    • Zhang Zhang [2016-05-08]
    • Guangyu Wang [2016-04-01]
    • Guangyu Wang [2015-11-24]
    • Guangyu Wang [2015-06-26]
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