title: Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.
abstract: Transcription factors control which information in a genome becomes transcribed to produce RNAs that function in the biological systems of cells and organisms. Reliable and comprehensive information about transcription factors is invaluable for large-scale network-based studies. However, existing transcription factor knowledge bases are still lacking in well-documented functional information. Here, we provide guidelines for a curation strategy, which constitutes a robust framework for using the controlled vocabularies defined by the Gene Ontology Consortium to annotate specific DNA binding transcription factors (DbTFs) based on experimental evidence reported in literature. Our standardized protocol and workflow for annotating specific DNA binding RNA polymerase II transcription factors is designed to document high-quality and decisive evidence from valid experimental methods. Within a collaborative biocuration effort involving the user community, we are now in the process of exhaustively annotating the full repertoire of human, mouse and rat proteins that qualify as DbTFs in as much as they are experimentally documented in the biomedical literature today. The completion of this task will significantly enrich Gene Ontology-based information resources for the research community. Database URL: www.tfcheckpoint.org.
authors: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7489 Trondheim, Norway.
authors: Sushil
authors: S
authors: Tripathi
authors: Karen R
authors: KR
authors: Christie
authors: Rama
authors: R
authors: Balakrishnan
authors: Rachael
authors: R
authors: Huntley
authors: David P
authors: DP
authors: Hill
authors: Liv
authors: L
authors: Thommesen
authors: Judith A
authors: JA
authors: Blake
authors: Martin
authors: M
authors: Kuiper
authors: Astrid
authors: A
authors: Lægreid
mesh_terms: D000818:Animals; D001483:Base Sequence; D004268:DNA-Binding Proteins / Q000235:genetics*; D057225:Data Mining / Q000379:methods*; D005786:Gene Expression Regulation; D063990:Gene Ontology; D017930:Genes, Reporter; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation; D011485:Protein Binding; D012319:RNA Polymerase II / Q000378:metabolism; D051381:Rats; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D012319:RNA Polymerase II
references: Science. 1989 Jul 28;245(4916):371-8
references: 2667136
references: Cell. 2010 Apr 30;141(3):432-45
references: 20434984
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D52-7
references: 21115458
references: Nat Rev Genet. 2009 Apr;10(4):252-63
references: 19274049
references: Mol Cell Proteomics. 2002 Jun;1(6):472-8
references: 12169687
references: Eukaryot Cell. 2013 Jan;12(1):101-8
references: 23143685
references: Science. 2004 Dec 24;306(5705):2255-7
references: 15618518
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D120-4
references: 18158297
references: BMC Bioinformatics. 2011 Aug 05;12:325
references: 21819553
references: Development. 2006 Oct;133(20):4119-29
references: 16971476
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D91-4
references: 14681366
references: Nature. 2012 Sep 6;489(7414):83-90
references: 22955618
references: Genome Res. 2006 Dec;16(12):1445-54
references: 17053092
references: Genome Biol. 2009;10(3):R29
references: 19284633
references: Nucleic Acids Res. 2013 Jan;41(Database issue):D530-5
references: 23161678
references: Nat Rev Genet. 2010 Jun;11(6):426-37
references: 20421872
references: Nucleic Acids Res. 2002 Jan 1;30(1):312-7
references: 11752324
references: Interface Focus. 2012 Feb 6;2(1):55-64
references: 23386960
references: Nat Rev Genet. 2010 Feb;11(2):109-23
references: 20084085
references: Bioinformatics. 2002 Nov;18(11):1542-3
references: 12424129
references: Nat Rev Genet. 2012 Oct;13(10):720-31
references: 22986266
references: Genome Biol. 2012;13(3):R24
references: 22458515
references: Nat Genet. 2004 Jul;36(7):664
references: 15226743
references: Database (Oxford). 2013 Jan 17;2013:bas062
references: 23327938
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D841-6
references: 22121220
references: EMBO J. 2004 Oct 13;23(20):4051-60
references: 15372072
references: Crit Rev Biochem Mol Biol. 2006 May-Jun;41(3):105-78
references: 16858867
references: Eur J Biochem. 2004 Jul;271(14):2855-62
references: 15233782
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13
references: 18006570
references: Nat Biotechnol. 2004 Feb;22(2):177-83
references: 14755292
references: PLoS Comput Biol. 2009 Mar;5(3):e1000311
references: 19300475