MGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Wan, Shibiao ^a   Mak, Man Wai ^a   Kung, Sun Yuan ^b  

^a HONG KONG POLYTECHNIC UNIVERSITY   (Hong Kong)

^b Princeton University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; EUCLIDEAN SPACES; FEATURE REPRESENTATION; GENE ONTOLOGY; GO TERMS; MULTI-LABEL; MULTI-LABEL PROTEINS; PROTEIN SUBCELLULAR LOCALIZATION; SPEED UP; SUBCELLULAR LOCALIZATIONS; SUBCELLULAR LOCATION; SVM CLASSIFIERS;

FORECASTING; PROTEINS; VIRUSES;

SUPPORT VECTOR MACHINES;

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENE; GENETICS; INTRACELLULAR SPACE; METABOLISM; METHODOLOGY; PROTEIN DATABASE; SUPPORT VECTOR MACHINE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GENES; INTRACELLULAR SPACE; PROTEINS; SOFTWARE; SUPPORT VECTOR MACHINES;

MLCS; MLOWN;

EID: 84868295522     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-290     Document Type: Article

References (49)

1. Apweiler R. Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences. Brief Bioinformatics 2001, 2:9-18. 10.1093/bib/2.1.9, 11465066.
2. Chou KC, Cai YD. Predicting protein localization in budding yeast. Bioinformatics 2005, 21:944-950. 10.1093/bioinformatics/bti104, 15513989.
3. Nakai K, Kanehisa M. Expert system for predicting protein localization sites in gram-negative bacteria. Proteins: Struct Funct Genet 1991, 11(2):95-110.
4. Horton P, Park KJ, Obayashi T. Protein subcellular localization prediction with WOLF PSORT. Proc. 4th Annual Asia Pacific Bioinformatics Conference (APBC06) 2006, 39-48.
5. Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 2000, 300(4):1005-1016. 10.1006/jmbi.2000.3903, 10891285.
6. Nielsen H, Engelbrecht J, Brunak S, von Heijne G. A neural network method for identification of prokaryotic and eukaryotic signal perptides and prediction of their cleavage sites. Int J Neural Sys 1997, 8:581-599.
7. Nielsen H, Brunak S, von Heijne G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng 1999, 12:3-9. 10.1093/protein/12.1.3, 10065704.
8. Nakashima H, Nishikawa K. Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies. J Mol Biol 1994, 238:54-61. 10.1006/jmbi.1994.1267, 8145256.
9. Park KJ, Kanehisa M. Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics 2003, 19(13):1656-1663. 10.1093/bioinformatics/btg222, 12967962.
10. Lee KY, Kim DW, Na DK, Lee KH, Lee DH. PLPD: Reliable protein localization prediction from imbalanced and overlapped datasets. Nucl Acids Res 2006, 34(17):4655-4666. 10.1093/nar/gkl638, 1636404, 16966337.
11. Chou KC. Prediction of protein cellular attributes using pseudo amino acid composition. Proteins: Struct Funct Genet 2001, 43:246-255.
12. Chou KC, Cai YD. Prediction and classification of protein subcellular location: sequence-order effect and pseudo amino acid composition. J Cell Biochem 2003, 90:1250-1260. 10.1002/jcb.10719, 14635197.
13. Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C, Eisner R. Predicting subcellular localization of proteins using machine-learned classifiers. Bioinformatics 2004, 20(4):547-556. 10.1093/bioinformatics/btg447, 14990451.
14. Mak MW, Guo J, Kung SY. PairProSVM: protein subcellular localization based on local pairwise profile alignment and SVM. IEEE/ACM Trans Comput Biol Bioinformatics 2008, 5(3):416-422.
15. Nair R, Rost B. Sequence conserved for subcellular localization. Protein Sci 2002, 11:2836-2847. 2373743, 12441382.
16. Mott R, Schultz J, Bork P, Ponting C. Predicting protein cellular localization using a domain projection method. Genome Res 2002, 12(8):1168-1174. 10.1101/gr.96802, 186639, 12176924.
17. Scott M, Thomas D, Hallett M. Predicting subcellular localization via protein motif co-occurrence. Genome Res 2004, 14(10a):1957-1966. 10.1101/gr.2650004, 524420, 15466294.
18. Camon E, Magrane M, Barrel D, Binns D, Fleischnann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R. The Gene Ontology annotation (GOA) project: Implementation of GO in SWISS-PROT, TrEMBL and InterPro. Genome Res 2003, 13:662-672. 10.1101/gr.461403, 430163, 12654719.
19. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Ntale DA, O'Donovan C, Redaschi N, Yeh LS. UniProt: the Universal Protein knowledgebase. Nucl Acids Res 2004, 32:D115-D119. 10.1093/nar/gkh131, 308865, 14681372.
20. Zdobnov EM, Apweiler R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848. 10.1093/bioinformatics/17.9.847, 11590104.
21. Chou KC, Cai YD. Prediction of protein subcellular locations by GO-FunD-PseAA predicor. Biochem Biophys Res Commun 2004, 320:1236-1239. 10.1016/j.bbrc.2004.06.073, 15249222.
22. Blum T, Briesemeister S, Kohlbacher O. MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics 2009, 10:274. 10.1186/1471-2105-10-274, 2745392, 19723330.
23. Wan S, Mak MW, Kung SY. Protein subcellular localization prediction based on profile alignment and Gene Ontology. 2011 IEEE International Workshop on Machine Learning for Signal Processing (MLSP'11) 2011,
24. Mei SY, Fei W, Zhou SG. Gene Ontology based transfer learning for protein subcellular localization. BMC Bioinformatics 2011, 12:44. 10.1186/1471-2105-12-44, 3039576, 21284890.
25. He J, Gu H, Liu W. Imbalanced multi-modal multi-label learning for subcellular localization prediction of human proteins with both single and multiple sites. PLoS ONE 2011, 7(6):e37155.
26. Chou KC, Shen HB. Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest neighbor classifiers. J Proteome Res 2006, 5:1888-1897. 10.1021/pr060167c, 16889410.
27. Chou KC, Shen HB. Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization. Biochem Biophys Res Commun 2006, 347:150-157. 10.1016/j.bbrc.2006.06.059, 16808903.
28. Chou KC, Shen HB. Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. J Proteome Res 2007, 6:1728-1734. 10.1021/pr060635i, 17397210.
29. Chou KC, Shen HB. Large-scale predictions of gram-negative bacterial protein subcellular locations. J Proteome Res 2006, 5:3420-3428. 10.1021/pr060404b, 17137343.
30. Tung TQ, Lee D. A method to improve protein subcellular localization prediction by integrating various biological data sources. BMC Bioinformatics 2009, 10(Suppl 1):S43. 10.1186/1471-2105-10-S1-S43, 2648781, 19208145.
31. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
32. Huang WL, Tung CW, Ho SW, Hwang SF, Ho SY. ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC Bioinformatics 2008, 9(80).
33. Xiao X, Wu ZC, Chou KC. iLoc-Virus: A multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites. J Theor Biol 2011, 284:42-51. 10.1016/j.jtbi.2011.06.005, 21684290.
34. Xiao X, Wu ZC, Chou KC. A multi-label learning classifier for predicting the subcellular localization of gram-negative bacterial proteins with both single and multiple sites. PLoS ONE 2011, 6(6):e20592. 10.1371/journal.pone.0020592, 3117797, 21698097.
35. Chou KC, Shen HB. Cell-PLoc 2.0: An improved package of web-servers for predicting subcellular localization of proteins in various organisms. Nat Sci 2010, 2:1090-1103.
36. Mueller JC, Andreoli C, Prokisch H, Meitinger T. Mechanisms for multiple intracellular localization of human mitochondrial proteins. Mitochondrion 2004, 3:315-325. 10.1016/j.mito.2004.02.002, 16120363.
37. Shen HB, Chou KC. Virus-mPLoc: a fusion classifier for viral protein subcellular location prediction by incorporating multiple sites. J Biomol Struct Dyn 2010, 26:175-186.
38. Shen HB, Chou KC. Virus-PLoc: A fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells. Biopolymers 2006, 85:233-240.
39. Li LQ, Zhang Y, Zou LY, Zhou Y, Zheng XQ. Prediction of protein subcellular multi-localization based on the general form of Chou's pseudo amino acid composition. Protein Peptide Lett 2012, 19:375-387.
40. Small I, Peeters N, Legeai F, Lurin C. Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 2004, 4:1581-1590. 10.1002/pmic.200300776, 15174128.
41. Chou KC, Shen HB. Plant-mPLoc: A top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS ONE 2010, 5:e11335. 10.1371/journal.pone.0011335, 2893129, 20596258.
42. Wu ZC, Xiao X, Chou KC. iLoc-Plant: A multi-label classifier for predicting the subcellular localization of plant proteins with both single and multiple sites. Mol BioSyst 2011, 7:3287-3297. 10.1039/c1mb05232b, 21984117.
43. Lord PW, Stevens RD, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003, 19(10):1275-1283. 10.1093/bioinformatics/btg153, 12835272.
44. Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R. QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics 2009, 25(22):3045-3046. 10.1093/bioinformatics/btp536, 2773257, 19744993.
45. Hastie T, Friedman J, Tibshirani R. The Element of Statistical Learning 2001, New York: Springer-Verlag.
46. Chou KC, Shen HB. Recent progress in protein subcellular location prediction. Anal Biochem 2007, 1(370):1-16.
47. Bhasin M, Raghava GPS. ESLpred: SVM based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic Acids Res 2004, 32(Webserver Issue):414-419.
48. Bengio Y, Delalleau O, Roux NL. The curse of dimensionality for local kernel machines. Tech. rep., Universite de Montreal 2005.
49. Tsoumakas G, Katakis I. Multi-label classification: An overview. Int J Data Warehousing Min 2007, 3:1-13.