title: GOPred: GO molecular function prediction by combined classifiers.
abstract: Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines different methods to better represent protein function. First, we formulated the function annotation problem as a classification problem defined on 300 different Gene Ontology (GO) terms from molecular function aspect. We presented a method to form positive and negative training examples while taking into account the directed acyclic graph (DAG) structure and evidence codes of GO. We applied three different methods and their combinations. Results show that combining different methods improves prediction accuracy in most cases. The proposed method, GOPred, is available as an online computational annotation tool (http://kinaz.fen.bilkent.edu.tr/gopred).
authors.affiliation: Department of Computer Engineering, Middle East Technical University, Ankara, Turkey.
authors.forename: Omer Sinan
authors.initials: OS
authors.lastname: Saraç
authors.forename: Volkan
authors.initials: V
authors.lastname: Atalay
authors.forename: Rengul
authors.initials: R
authors.lastname: Cetin-Atalay
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006801:Humans; D020407:Internet; D011506:Proteins / Q000145:classification* / Q000378:metabolism*
chemical_list: D011506:Proteins
references.citation: Gene. 2008 May 31;415(1-2):60-7
references.pmid: 18403135
references.citation: Proteins. 2005 Mar 1;58(4):955-70
references.pmid: 15645499
references.citation: Comput Biol Chem. 2008 Apr;32(2):122-30
references.pmid: 18243801
references.citation: Protein Sci. 2006 Jun;15(6):1550-6
references.pmid: 16672240
references.citation: Trends Genet. 2000 Jun;16(6):276-7
references.pmid: 10827456
references.citation: Antioxid Redox Signal. 2004 Feb;6(1):63-74
references.pmid: 14713336
references.citation: Cancer Res. 2006 Feb 1;66(3):1346-53
references.pmid: 16452188
references.citation: Mol Cell Biol. 1986 Feb;6(2):730-4
references.pmid: 3537694
references.citation: Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5396-401
references.pmid: 18385383
references.citation: Bioinformatics. 2008 Mar 15;24(6):798-806
references.pmid: 18263643
references.citation: Cells Tissues Organs. 2008;188(1-2):91-102
references.pmid: 18196925
references.citation: BMC Bioinformatics. 2004 Nov 18;5:178
references.pmid: 15550167
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Math Biosci. 2005 Feb;193(2):223-34
references.pmid: 15748731
references.citation: Yeast. 2000 Dec;17(4):283-93
references.pmid: 11119305
references.citation: Protein Sci. 2006 Jun;15(6):1557-62
references.pmid: 16672244
references.citation: Bioinformatics. 2003;19 Suppl 1:i26-33
references.pmid: 12855434
references.citation: J Comput Biol. 2005;12(1):64-82
references.pmid: 15725734
references.citation: Bioinformatics. 2004 Mar 1;20(4):467-76
references.pmid: 14990442
references.citation: J Biol Chem. 2004 Apr 2;279(14):14256-63
references.pmid: 14734546
references.citation: J Mol Biol. 2002 Jun 21;319(5):1257-65
references.pmid: 12079362
references.citation: PLoS Comput Biol. 2005 Oct;1(5):e45
references.pmid: 16217548
references.citation: BMC Bioinformatics. 2008 Sep 22;9:389
references.pmid: 18808707
references.citation: J Mol Biol. 2000 Oct 13;303(1):61-76
references.pmid: 11021970
references.citation: Nat Rev Cancer. 2008 Feb;8(2):133-40
references.pmid: 18219307
references.citation: Cell. 1992 Aug 21;70(4):523-6
references.pmid: 1505019
references.citation: Proteins. 2001 Aug 15;44(3):361-9
references.pmid: 11455609
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D154-9
references.pmid: 15608167
references.citation: Proteins. 2000 Oct 1;41(1):98-107
references.pmid: 10944397
references.citation: BMC Genomics. 2009 May 28;10:250
references.pmid: 19476624
references.citation: Bioinformatics. 2002 Jan;18(1):147-59
references.pmid: 11836223
references.citation: Blood. 1970 Aug;36(2):219-27
references.pmid: 5427456
references.citation: Proc IEEE Comput Syst Bioinform Conf. 2005;:80-5
references.pmid: 16447965
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3692-7
references.pmid: 12824396
references.citation: Trends Cell Biol. 2005 Feb;15(2):112-20
references.pmid: 15695098
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Brief Bioinform. 2006 Sep;7(3):225-42
references.pmid: 16772267