TFClass: expanding the classification of human transcription factors to their mammalian orthologs

Nucleic Acids Research
Edgar WingenderJürgen Dönitz

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.

References

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Dec 3, 2016·Nucleic Acids Research·UNKNOWN The UniProt Consortium

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Citations

Dec 21, 2018·Genome Research·Hongyang LiYuanfang Guan
Jul 15, 2020·The Journal of Immunology : Official Journal of the American Association of Immunologists·Mei San TangP'ng Loke
Jan 27, 2019·Nature Communications·Gregory J FonsecaChristopher K Glass
Apr 17, 2020·Cells·Juan Carlos González-OrozcoIgnacio Camacho-Arroyo
Mar 28, 2019·Science China. Life Sciences·Marten Kellner, Wojciech Makałowski
Jul 13, 2019·F1000Research·Benjamin J StubbsVincent Carey
Nov 25, 2018·International Journal of Molecular Sciences·Zhaojiang GuoYoujun Zhang
Jul 7, 2018·NPJ Systems Biology and Applications·Stephen Wilson, Fabian Volker Filipp
Oct 3, 2018·Wiley Interdisciplinary Reviews. RNA·Toshimichi Yamada, Nobuyoshi Akimitsu
Nov 9, 2019·Nucleic Acids Research·Oriol FornesAnthony Mathelier
Aug 23, 2020·International Journal of Molecular Sciences·Victor LevitskyTatyana Merkulova
Oct 21, 2020·Scientific Reports·Sebastian Carrasco ProJuan Ignacio Fuxman Bass
Oct 24, 2020·Nucleic Acids Research·Qi PanChun-Quan Li
Nov 25, 2020·Nucleic Acids Research·Semyon KolmykovFedor Kolpakov
Mar 21, 2021·Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology·Kanaka Sai Ram PadamRaghu Radhakrishnan
Sep 29, 2021·Genome Biology·Gherman NovakovskyWyeth W Wasserman
Oct 8, 2021·Nature·Hanqing LiuJoseph R Ecker

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