An ensemble classifier for eukaryotic protein subcellular location prediction using gene ontology categories and amino acid hydrophobicity

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Li, Liqi ^a   Zhang, Yuan ^a   Zou, Lingyun ^a   Li, Changqing ^a   Yu, Bo ^b   Zheng, Xiaoqi ^c   Zhou, Yue ^a  

^a THIRD MILITARY MEDICAL UNIVERSITY   (China)

^b Department of Orthopedics   (China)

^c SHANGHAI NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; EUKARYOTIC PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

ACCURACY; ALGORITHM; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; CELLULAR DISTRIBUTION; CLASSIFIER; HUMAN; HYDROPHOBICITY; INTERMETHOD COMPARISON; K NEAREST NEIGHBOR; MACHINE LEARNING; NONHUMAN; PREDICTION; PROTEIN LOCALIZATION; SUPPORT VECTOR MACHINE; CELL FRACTIONATION; CHEMICAL PHENOMENA; EUKARYOTIC CELL; GENE; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN DATABASE;

EUKARYOTA;

ALGORITHMS; AMINO ACIDS; DATABASES, PROTEIN; EUKARYOTIC CELLS; GENES; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MOLECULAR SEQUENCE ANNOTATION; PROTEINS; SUBCELLULAR FRACTIONS; SUPPORT VECTOR MACHINES;

EID: 84856376845     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031057     Document Type: Article

References (62)

1. Laurila K, Vihinen M, (2011) PROlocalizer: integrated web service for protein subcellular localization prediction. Amino Acids 40: 975-980.
2. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, et al. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26: 1608-1615.
3. Shen YQ, Burger G, (2010) TESTLoc: protein subcellular localization prediction from EST data. BMC Bioinformatics 11: 563.
4. Chou KC, Shen HB, (2010) Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS One 5: e11335.
5. Wang W, Geng X, Dou Y, Liu T, Zheng X, (2011) Predicting protein subcellular localization by pseudo amino acid composition with a segment-weighted and features-combined approach. Protein Pept Lett 18: 480-487.
6. Nakashima H, Nishikawa K, (1994) Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies. J Mol Biol 238: 54-61.
7. Gu Q, Ding YS, Jiang XY, Zhang TL, (2010) Prediction of subcellular location apoptosis proteins with ensemble classifier and feature selection. Amino Acids 38: 975-983.
8. Park KJ, Kanehisa M, (2003) Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics 19: 1656-1663.
9. Rao HB, Zhu F, Yang GB, Li ZR, Chen YZ, (2011) Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res 39 (Suppl 2): W385-390.
10. Jia P, Qian Z, Zeng Z, Cai Y, Li Y, (2007) Prediction of subcellular protein localization based on functional domain composition. Biochem Biophys Res Commun 357: 366-370.
11. Guo J, Pu X, Lin Y, Leung H, (2006) Protein subcellular localization based on PSI-BLAST and machine learning. J Bioinform Comput Biol 4: 1181-1195.
12. Bhasin M, Raghava GP, (2004) ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic Acids Res 32: W414-419.
13. Emanuelsson O, Nielsen H, Brunak S, von Heijne G, (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016.
14. Emanuelsson O, Brunak S, von Heijne G, Nielsen H, (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2: 953-971.
15. Rashid M, Saha S, Raghava GP, (2007) Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs. BMC Bioinformatics 8: 337.
16. Lin TH, Murphy RF, Bar-Joseph Z, (2011) Discriminative motif finding for predicting protein subcellular localization. IEEE/ACM Trans Comput Biol Bioinform 8: 441-451.
17. Zou L, Wang Z, Huang J, (2007) Prediction of subcellular localization of eukaryotic proteins using position-specific profiles and neural network with weighted inputs. J Genet Genomics 34: 1080-1087.
18. Wang T, Yang J, (2010) Predicting subcellular localization of gram-negative bacterial proteins by linear dimensionality reduction method. Protein Pept Lett 17: 32-37.
19. Liao B, Jiang JB, Zeng QG, Zhu W, (2011) Predicting Apoptosis Protein Subcellular Location with PseAAC by Incorporating Tripeptide Composition. Protein Pept Lett 18: 1086-1092.
20. Mount DW, (2009) Using hidden Markov models to align multiple sequences. Cold Spring Harb Protoc 2009: pdb top41.
21. Marinov M, Weeks DE, (2001) The complexity of linkage analysis with neural networks. Hum Hered 51: 169-176.
22. Shen HB, Yang J, Chou KC, (2007) Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction. Amino Acids 33: 57-67.
23. Bulashevska A, Eils R, (2006) Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains. BMC Bioinformatics 7: 298.
24. Khan A, Majid A, Hayat M, (2011) CE-PLoc: an ensemble classifier for predicting protein subcellular locations by fusing different modes of pseudo amino acid composition. Comput Biol Chem 35: 218-229.
25. Li LQ, Kuang H, Zhang Y, Zhou Y, Wang KF, et al. (2011) Prediction of eukaryotic protein subcellular multilocalisation with a combined KNN-SVM ensemble classifier. Journal of Computational Biology and Bioinformatics Research 3: 15-24.
26. Yu X, Zheng X, Liu T, Dou Y, Wang J, (2011) Predicting subcellular location of apoptosis proteins with pseudo amino acid composition: approach from amino acid substitution matrix and auto covariance transformation. Amino Acids [Epub ahead of print].
27. Wang P, Hu L, Liu G, Jiang N, Chen X, et al. (2011) Prediction of antimicrobial peptides based on sequence alignment and feature selection methods. PLoS One 6: e18476.
28. Huang T, Chen L, Cai YD, Chou KC, (2011) Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PLoS One 6: e25297.
29. Huang T, Wan S, Xu Z, Zheng Y, Feng KY, et al. (2011) Analysis and prediction of translation rate based on sequence and functional features of the mRNA. PLoS One 6: e16036.
30. Chou KC, Wu ZC, Xiao X, (2011) iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins. PLoS One 6: e18258.
31. Shen HB, Chou KC, (2009) A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0. Anal Biochem 394: 269-274.
32. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-261.
33. Lei Z, Dai Y, (2006) Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction. BMC Bioinformatics 7: 491.
34. Seo MJ, Bae SM, Kim YW, Hur SY, Ro DY, et al. (2005) New approaches to pathogenic gene function discovery with human squamous cell cervical carcinoma by gene ontology. Gynecol Oncol 96: 621-629.
35. Currie RA, Orphanides G, Moggs JG, (2005) Mapping molecular responses to xenoestrogens through Gene Ontology and pathway analysis of toxicogenomic data. Reprod Toxicol 20: 433-440.
36. Cai YD, Zhou GP, Chou KC, (2005) Predicting enzyme family classes by hybridizing gene product composition and pseudo-amino acid composition. J Theor Biol 234: 145-149.
37. Qian Z, Cai YD, Li Y, (2006) A novel computational method to predict transcription factor DNA binding preference. Biochem Biophys Res Commun 348: 1034-1037.
38. Chou KC, Shen HB, (2010) A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0. PLoS One 5: e9931.
39. Huang WL, Tung CW, Huang HL, Ho SY, (2009) Predicting protein subnuclear localization using GO-amino-acid composition features. Biosystems 98: 73-79.
40. Mei S, Fei W, Zhou S, (2011) Gene ontology based transfer learning for protein subcellular localization. BMC Bioinformatics 12: 44.
41. Sahu SS, Panda G, (2010) A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction. Comput Biol Chem 34: 320-327.
42. Khan A, Majid A, Choi TS, (2010) Predicting protein subcellular location: exploiting amino acid based sequence of feature spaces and fusion of diverse classifiers. Amino Acids 38: 347-350.
43. Zhou XB, Chen C, Li ZC, Zou XY, (2008) Improved prediction of subcellular location for apoptosis proteins by the dual-layer support vector machine. Amino Acids 35: 383-388.
44. Smith TF, (1980) Occam's razor. Nature 285: 620.
45. Qiu JD, Luo SH, Huang JH, Sun XY, Liang RP, (2010) Predicting subcellular location of apoptosis proteins based on wavelet transform and support vector machine. Amino Acids 38: 1201-1208.
46. Cai YD, Chou KC, (2000) Using neural networks for prediction of subcellular location of prokaryotic and eukaryotic proteins. Mol Cell Biol Res Commun 4: 172-173.
47. Yu NY, Laird MR, Spencer C, Brinkman FS, (2011) PSORTdb-an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea. Nucleic Acids Res 39: D241-244.
48. Pierleoni A, Martelli PL, Casadio R, (2011) MemLoci: predicting subcellular localization of membrane proteins in eukaryotes. Bioinformatics 27: 1224-1230.
49. Xu Q, Pan SJ, Xue HH, Yang Q, (2011) Multitask learning for protein subcellular location prediction. IEEE/ACM Trans Comput Biol Bioinform 8: 748-759.
50. Wang J, Li C, Wang E, Wang X, (2011) An FPT approach for predicting protein localization from yeast genomic data. PLoS One 6: e14449.
51. Yuan Z, (1999) Prediction of protein subcellular locations using Markov chain models. FEBS Lett 451: 23-26.
52. Shi R, Xu C, (2011) Prediction of rat protein subcellular localization with pseudo amino acid composition based on multiple sequential features. Protein Pept Lett 18: 625-633.
53. Panwar B, Raghava GP, (2011) Predicting sub-cellular localization of tRNA synthetases from their primary structures. Amino Acids [Epub ahead of print].
54. Kim JK, Raghava GPS, Bang SY, Choi SJ, (2006) Prediction of subcellular localization of proteins using pairwise sequence alignment and support vector machine. Pattern Recognition Letters 27: 996-1001.
55. Chou KC, Shen HB, (2008) Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nat Protoc 3: 153-162.
56. Shi SP, Qiu JD, Sun XY, Huang JH, Huang SY, et al. (2011) Identify submitochondria and subchloroplast locations with pseudo amino acid composition: approach from the strategy of discrete wavelet transform feature extraction. Biochim Biophys Acta 1813: 424-430.
57. Ansari HR, Raghava GP, (2010) Identification of NAD interacting residues in proteins. BMC Bioinformatics 11: 160.
58. Xie D, Li A, Wang M, Fan Z, Feng H, (2005) LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST. Nucleic Acids Res 33: W105-110.
59. Zheng X, Liu T, Wang J, (2009) A complexity-based method for predicting protein subcellular location. Amino Acids 37: 427-433.
60. Chou KC, Shen HB, (2007) Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. J Proteome Res 6: 1728-1734.
61. Zhang Y, Xiang Q, Dong S, Li C, Zhou Y, (2010) Fabrication and characterization of a recombinant fibronectin/cadherin bio-inspired ceramic surface and its influence on adhesion and ossification in vitro. Acta Biomater 6: 776-785.
62. Zhang Y, Zhou Y, Zhu J, Dong S, Li C, et al. (2009) Effect of a novel recombinant protein of fibronectinIII7-10/cadherin 11 EC1-2 on osteoblastic adhesion and differentiation. Biosci Biotechnol Biochem 73: 1999-2006.