TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins

Handle URI:
http://hdl.handle.net/10754/334582
Title:
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins
Authors:
Schaefer, Ulf; Schmeier, Sebastian; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
The initiation and regulation of transcription in eukaryotes is complex and involves a large number of transcription factors (TFs), which are known to bind to the regulatory regions of eukaryotic DNA. Apart from TF-DNA binding, protein-protein interaction involving TFs is an essential component of the machinery facilitating transcriptional regulation. Proteins that interact with TFs in the context of transcription regulation but do not bind to the DNA themselves, we consider transcription co-factors (TcoFs). The influence of TcoFs on transcriptional regulation and initiation, although indirect, has been shown to be significant with the functionality of TFs strongly influenced by the presence of TcoFs. While the role of TFs and their interaction with regulatory DNA regions has been well-studied, the association between TFs and TcoFs has so far been given less attention. Here, we present a resource that is comprised of a collection of human TFs and the TcoFs with which they interact. Other proteins that have a proven interaction with a TF, but are not considered TcoFs are also included. Our database contains 157 high-confidence TcoFs and additionally 379 hypothetical TcoFs. These have been identified and classified according to the type of available evidence for their involvement in transcriptional regulation and their presence in the cell nucleus. We have divided TcoFs into four groups, one of which contains high-confidence TcoFs and three others contain TcoFs which are hypothetical to different extents. We have developed the Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins (TcoF-DB). A web-based interface for this resource can be freely accessed at http://cbrc.kaust.edu.sa/tcof/ and http://apps.sanbi.ac.za/tcof/. © The Author(s) 2010.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Schaefer U, Schmeier S, Bajic VB (2010) TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Research 39: D106-D110. doi:10.1093/nar/gkq945.
Publisher:
Oxford University Press
Journal:
Nucleic Acids Research
Issue Date:
21-Oct-2010
DOI:
10.1093/nar/gkq945
PubMed ID:
20965969
PubMed Central ID:
PMC3013796
Type:
Article
ISSN:
0305-1048
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorSchaefer, Ulfen
dc.contributor.authorSchmeier, Sebastianen
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2014-11-11T14:30:42Z-
dc.date.available2014-11-11T14:30:42Z-
dc.date.issued2010-10-21en
dc.identifier.citationSchaefer U, Schmeier S, Bajic VB (2010) TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Research 39: D106-D110. doi:10.1093/nar/gkq945.en
dc.identifier.issn0305-1048en
dc.identifier.pmid20965969en
dc.identifier.doi10.1093/nar/gkq945en
dc.identifier.urihttp://hdl.handle.net/10754/334582en
dc.description.abstractThe initiation and regulation of transcription in eukaryotes is complex and involves a large number of transcription factors (TFs), which are known to bind to the regulatory regions of eukaryotic DNA. Apart from TF-DNA binding, protein-protein interaction involving TFs is an essential component of the machinery facilitating transcriptional regulation. Proteins that interact with TFs in the context of transcription regulation but do not bind to the DNA themselves, we consider transcription co-factors (TcoFs). The influence of TcoFs on transcriptional regulation and initiation, although indirect, has been shown to be significant with the functionality of TFs strongly influenced by the presence of TcoFs. While the role of TFs and their interaction with regulatory DNA regions has been well-studied, the association between TFs and TcoFs has so far been given less attention. Here, we present a resource that is comprised of a collection of human TFs and the TcoFs with which they interact. Other proteins that have a proven interaction with a TF, but are not considered TcoFs are also included. Our database contains 157 high-confidence TcoFs and additionally 379 hypothetical TcoFs. These have been identified and classified according to the type of available evidence for their involvement in transcriptional regulation and their presence in the cell nucleus. We have divided TcoFs into four groups, one of which contains high-confidence TcoFs and three others contain TcoFs which are hypothetical to different extents. We have developed the Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins (TcoF-DB). A web-based interface for this resource can be freely accessed at http://cbrc.kaust.edu.sa/tcof/ and http://apps.sanbi.ac.za/tcof/. © The Author(s) 2010.en
dc.language.isoenen
dc.publisherOxford University Pressen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rightsArchived with thanks to Nucleic Acids Researchen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.5/en
dc.subjecttranscription co factoren
dc.subjecttranscription factoren
dc.subjectunclassified drugen
dc.subjectcell nucleusen
dc.subjectcomputer interfaceen
dc.subjectprotein analysisen
dc.subjectprotein databaseen
dc.subjectprotein localizationen
dc.subjectprotein protein interactionen
dc.subjectTcoF DBen
dc.subjecttranscription regulationen
dc.subjectweb browseren
dc.subjectCarrier Proteinsen
dc.subjectDatabases, Proteinen
dc.subjectProtein Interaction Mappingen
dc.subjectTranscription Factorsen
dc.subjectTranscription, Geneticen
dc.subjectEukaryotaen
dc.titleTcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteinsen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalNucleic Acids Researchen
dc.identifier.pmcidPMC3013796en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorSchmeier, Sebastianen
kaust.authorSchaefer, Ulfen
kaust.authorBajic, Vladimir B.en

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