TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions
Item Type Article
Authors Schmeier, Sebastian; Alam, Tanvir; Essack, Magbubah; Bajic, Vladimir B.
Citation Schmeier S, Alam T, Essack M, Bajic VB (2016) TcoF-DB v2: update of the database of human and mouse transcription co- factors and transcription factor interactions. Nucleic Acids Research: gkw1007. Available: http://dx.doi.org/10.1093/nar/ gkw1007.
Eprint version Publisher's Version/PDF
DOI 10.1093/nar/gkw1007
Publisher Oxford University Press (OUP)
Journal Nucleic Acids Research
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Item License http://creativecommons.org/licenses/by-nc/4.0/ Link to Item http://hdl.handle.net/10754/622045 Nucleic Acids Research, 2016 1 doi: 10.1093/nar/gkw1007 TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions Sebastian Schmeier1, Tanvir Alam2, Magbubah Essack2 and Vladimir B. Bajic2,*
1Massey University Auckland, Institute of Natural and Mathematical Sciences, Auckland, New Zealand and 2King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
Received August 29, 2016; Revised September 29, 2016; Editorial Decision October 15, 2016; Accepted October 17, 2016
ABSTRACT teins work in unison to facilitate the recruitment of RNA Polymerase II to the site of transcription initiation, which Transcription factors (TFs) play a pivotal role in substantially increases the complexity of the regulatory pro- transcriptional regulation, making them crucial for cess (10). TcoFs have many functions, such as signal trans- cell survival and important biological functions. For duction, modulation of TF–DNA binding, and chromatin the regulation of transcription, interactions of differ- modification (11,12). However, so far research on the inter- ent regulatory proteins known as transcription co- action of TFs with other proteins in relation to transcription factors (TcoFs) and TFs are essential in forming nec- regulation has not been that intensive. essary protein complexes. Although TcoFs them- Protein–protein interactions (PPI) play a crucial role in selves do not bind DNA directly, their influence on transcriptional regulation and can take several forms, e.g. transcriptional regulation and initiation, although in- the modification of one protein by another protein, thefor- direct, has been shown to be significant, with the mation of a protein complex by two or more proteins, etc. PPIs of our interest include the physical interaction between functionality of TFs strongly influenced by the pres- two TFs (10,13), the physical interaction between a TF and ence of TcoFs. In the TcoF-DB v2 database, we col- a TcoF, as well as potentially, the physical interaction be- lect information on TcoFs. In this article, we describe tween a TF and other nuclear proteins that are not known updates and improvements implemented in TcoF-DB to function as TFs or TcoFs. A web-based tool to recognise v2. TcoF-DB v2 provides several new features that the type of TF binding partner has also been developed (14). enables exploration of the roles of TcoFs. The con- Several resources that collect information on mam- tent of the database has significantly expanded, and malian TFs exist (e.g. JASPAR (15), TRANSFAC (16), is enriched with information from Gene Ontology, HOCOMOCO (17), TFCat (18), DBD (19), TFCONES biological pathways, diseases and molecular signa- (20), TFcheckpoint (21), TFdb (22), COMPEL (23), tures. TcoF-DB v2 now includes many more TFs; has TRANSCompel (16), etc.). While the influence of TFs on substantially increased the number of human TcoFs many biological processes (24–27) and diseases (26,28–30) is well established and described, research into the influ- to 958, and now includes information on mouse (418 ence of TcoFs has not received the same level of atten- new TcoFs). TcoF-DB v2 enables the exploration of tion. However, the recent release of the FARNA database information on TcoFs and allows investigations into (http://cbrc.kaust.edu.sa/farna) utilised TcoFs (31) to infer their influence on transcriptional regulation in hu- functions of over 10 000 non-coding transcripts in humans, mans and mice. TcoF-DB v2 can be accessed at showing the importance of TcoFs for the function of their http://tcofdb.org/. target transcripts. To facilitate investigations into the influ- ence of TcoFs on the regulation of transcriptional initia- tion, we first developed in 2010 the TcoF-DB database that INTRODUCTION comprises human TFs and 529 TcoFs that interact with Transcriptional regulation in eukaryotes is a complex pro- them (31). In 2014, 415 human TcoFs as well as TcoFs from cess. It involves many proteins that assemble at the site of other species were published in AnimalTFDB 2.0 database transcription initiation (1,2) either binding DNA directly, (32). However, we still do not know the complete list of e.g. transcription factors (TFs) (3–5), or interacting with TFs and TcoFs in mammals. Thus, we developed an up- TFs, e.g. transcription co-factors (TcoFs) (6–9). These pro- dated version of TcoF-DB v2, which increases the number
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