Enhancing membrane protein subcellular localization prediction by parallel fusion of multi-view features

IEEE Transactions on Nanobioscience

Volumn 11, Issue 4, 2012, Pages 375-385

  Yu, Dongjun ^a   Wu, Xiaowei ^a   Shen, Hongbin ^b   Yang, Jian ^a   Tang, Zhenmin ^a   Qi, Yong ^a   Yang, Jingyu ^a  

^a NANJING UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

Feature extraction; GPCA; membrane protein; parallel feature fusion; serial feature fusion; subcellular localization prediction

Indexed keywords

COMPLEX GEOMETRIES; COMPLEX SPACE; COMPUTATIONAL BIOLOGY; DATA SETS; FEATURE FUSION; FEATURE REDUCTION; FEATURE VECTORS; GENERALIZED PRINCIPLE COMPONENT ANALYSIS; GPCA; INFORMATION REDUNDANCIES; LIVING ORGANISMS; MEMBRANE PROTEINS; MULTI-VIEWS; PARALLEL FRAMEWORK; PARALLEL STRATEGIES; PARALLEL TECHNIQUES; PREDICTION ACCURACY; PRIMARY SEQUENCES; PROTEIN SAMPLES; PROTEIN SUBCELLULAR LOCATION; SOLUBLE PROTEINS; SUBCELLULAR LOCALIZATIONS; SUBCELLULAR LOCATION;

BIOINFORMATICS; BIOLOGY; FEATURE EXTRACTION; FORECASTING; LEARNING ALGORITHMS; LEARNING SYSTEMS; PARALLEL ARCHITECTURES; PRINCIPAL COMPONENT ANALYSIS; PROTEINS;

BIOLOGICAL MEMBRANES;

MEMBRANE PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; METABOLISM; PROTEIN DATABASE; PROTEIN TRANSPORT;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; DATABASES, PROTEIN; MEMBRANE PROTEINS; MODELS, BIOLOGICAL; PROTEIN TRANSPORT; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84870860627     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2012.2208473     Document Type: Article

References (55)

1. H. B. Shen, J. Yang, and K. C. Chou, "Euk-PLoc: An ensemble classifier for large-scale eukaryotic protein subcellular location prediction, " Amino Acids, vol. 33, no. 1, pp. 57-67, Jul. 2007. (Pubitemid 47101466)
2. R. Casadio, P. L. Martelli, and A. Pierleoni, "The prediction of protein subcellular localization from sequence: A shortcut to functional genome annotation, " Brief Funct. Genomic Proteomic, vol. 7, no. 1, pp. 63-73, 2008. (Pubitemid 351721151)
3. A. Pierleoni, P. L. Martelli, and R. Casadio, "MemLoci: Predicting subcellular localization of membrane proteins in eukaryotes, " Bioinformatics, vol. 27, no. 9, pp. 1224-1230, 2011.
4. H. J. Sharpe, T. J. Stevens, and S. Munro, "A comprehensive comparison of transmembrane domains reveals organelle-specific properties, " Cell, vol. 142, no. 1, pp. 158-169, 2010.
5. K. Nakai, "Protein sorting signals and prediction of subcellular localization, " Adv. Protein Chem., vol. 54, pp. 277-344, 2000. (Pubitemid 30458951)
6. P. Horton et al., "WoLF PSORT: Protein localization predictor, " Nucleic Acids Res., vol. 35, no. 2, pp. W585-W587, Jul. 2007.
7. C. Guda and S. Subramaniam, "pSTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes, " Bioinformatics, vol. 21, no. 21, pp. 3963-3969, 2005. (Pubitemid 41631835)
8. S. Briesemeister, J. Rahnenfuhrer, and O. Kohlbacher, "YLoc-An interpretable web server for predicting subcellular localization, " Nucleic Acids Res., vol. 38, no. 2, pp. W497-502, 2010.
9. K. Imai and K. Nakai, "Prediction of subcellular locations of proteins: Shere to proceed, " Proteomics, vol. 10, no. 22, pp. 3970-3983, 2010.
10. S. Briesemeister, J. Rahnenfuhrer, and O. Kohlbacher, "Going from where to why-Interpretable prediction of protein subcellular localization, " Bioinformatics, vol. 26, no. 9, pp. 1232-1238, 2010.
11. O. Emanuelsson et al., "Locating proteins in the cell using targetp, signalp and related tools, " Nature Protocols, vol. 2, no. 4, pp. 953-971, 2007. (Pubitemid 46745592)
12. K. C. Chou and H. B. Shen, "Cell-PLoc: A package of web servers for predicting subcellular localization of proteins in various organisms, " Nature Protocols, vol. 3, no. 2, pp. 153-162, 2008.
13. A. Khan, A. Majid, and M. Hayat, "CE-PLoc: An ensemble classifier for predicting protein subcellular locations by fusing different modes of pseudo amino acid composition, " Comput. Biol. Chem., vol. 35, no. 4, pp. 218-229, 2011.
14. A. Khan, A. Majid, and T. S. Choi, "Predicting protein subcellular location: Exploiting amino acid based sequence of feature spaces and fusion of diverse classifiers, " Amino Acids, vol. 38, no. 1, pp. 347-350, 2010.
15. K. C. Chou and D. W. Elrod, "Prediction of membrane protein types and subcellular locations, " Proteins, vol. 34, no. 1, pp. 137-153, 1999. (Pubitemid 29019537)
16. K. C. Chou and D. W. Elrod, "Protein subcellular location prediction, " Protein Eng., vol. 12, no. 2, pp. 107-118, 1999. (Pubitemid 29103689)
17. C. Chen et al., "Predicting protein structural class based on multi-features fusion, " J. Theor. Biol., vol. 253, no. 2, pp. 388-392, 2008.
18. J. C. Jeong, X. Lin, and X. W. Chen, "On position-specific scoring matrix for protein function prediction, " IEEE/ACM Trans. Comput. Biol. Bioinformatics, vol. 8, no. 2, pp. 308-315, 2011.
19. R. Kohavi and G. H. John, "Wrappers for feature subset selection, " Artif. Intell., vol. 97, pp. 273-324, 1997. (Pubitemid 127401107)
20. J. Yang et al., "Feature fusion: Parallel strategy vs. serial strategy, " Pattern Recogn., vol. 36, no. 6, pp. 1369-1381, 2003. (Pubitemid 36225872)
21. K. Pearson, "On lines and planes of closest fit to systems of points in space, " Philos. Mag., vol. 2, no. 6, pp. 559-572, 1901.
22. M. S. Scott et al., "Refining protein subcellular localization, " PLoS Comput. Biol., vol. 1, no. 6, p. E66, 2005.
23. B. Boeckmann et al., "The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003, " Nucleic Acids Res., vol. 31, no. 1, pp. 365-370, 2003. (Pubitemid 36157284)
24. K. C. Chou, "Prediction of protein cellular attributes using pseudoamino acid composition, " Proteins, vol. 43, no. 3, pp. 246-255, 2001.
25. H. B. Shen and K. C. Chou, "PseAAC: A flexible web server for generating various kinds of protein pseudo amino acid composition, " Anal. Biochem., vol. 373, no. 2, pp. 386-8, Feb. 2008.
26. H. J. Hu et al., "To be or not to be: Predicting soluble secas as membrane proteins, " IEEE Trans. NanoBiosci., vol. 6, no. 2, pp. 168-179, 2007.
27. S. A. Chen et al., "Prediction of transporter targets using efficient rbf networks with PSSM profiles and biochemical properties, " Bioinformatics, vol. 27, no. 15, pp. 2062-2067, 2011.
28. Y. Y. Ou, S. A. Chen, and M. M. Gromiha, "Classification of transporters using efficient radial basis function networks with position-specific scoring matrices and biochemical properties, " Proteins, vol. 78, no. 7, pp. 1789-1797, 2010.
29. M. Amico et al., "PONGO: A web server for multiple predictions of all-alpha transmembrane proteins, " Nucleic Acids Res., vol. 34, no. 2, pp. W169-W172, 2006. (Pubitemid 44529757)
30. D. J. Yu, H. B. Shen, and J. Y. Yang, "SOMRuler:Anovel interpretable transmembrane helices predictor, " IEEE Trans. NanoBiosci., vol. 10, no. 2, pp. 121-129, 2011.
31. K. Chen and L. P. Kurgan, "Protein fold classification by using evolutionary information and predicted secondary structure, " Bioinformatics, vol. 23, no. 21, pp. 2843-2850, 2007. (Pubitemid 350162889)
32. M. N. Nguyen, J. M. Zurada, and J. C. Rajapakse, "Toward better understanding of protein secondary structure: Extracting prediction rules, " IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 8, no. 3, pp. 858-864, 2011.
33. M. Kumar, M. M. Gromiha, and G. P. Raghava, "Prediction of RNA binding sites in a protein using SVMand PSSM profile, " Proteins, vol. 71, no. 1, pp. 189-194, 2008. (Pubitemid 351358602)
34. M. Kumar, M. M. Gromiha, and G. P. Raghava, "SVM based prediction of RNA-binding proteins using binding residues and evolutionary information, " J Mol. Recognit., vol. 24, no. 2, pp. 303-313, 2011.
35. T. Zhang et al., "Analysis and prediction of RNA-binding residues using sequence, evolutionary conservation, and predicted secondary structure and solvent accessibility, " Curr. Protein Pept. Sci., vol. 11, no. 7, pp. 609-628, 2010.
36. L. Bartoli et al., "CCHMM-PROF: A HMM-based coiled-coil predictor with evolutionary information, " Bioinformatics, vol. 25, no. 21, pp. 2757-2763, 2009.
37. C. T. Su, C. Y. Chen, and Y. Y. Ou, "Protein disorder prediction by condensed PSSM considering propensity for order or disorder, " BMC Bioinformatics, vol. 7, p. 319, 2006.
38. A. A. Schaffer, "Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements, " Nucleic Acids Res., vol. 29, pp. 2994-3005, 2001. (Pubitemid 32685225)
39. S. Wold et al., "DNA and peptide sequences and chemical processes multivariately modeled by principal component analysis and partial leastsquares projections to latent structures, " Anal. Chim. Acta, vol. 277, no. 2, pp. 239-253, 1993. (Pubitemid 23158002)
40. T. Liu et al., "Accurate prediction of protein structural class using auto covariance transformation of PSI-BLAST profiles, " Amino Acids, vol. 42, no. 6, pp. 2243-2249, 2012.
41. X. R. Ding and M. K. Cai, Matrix Theory in Engineering. Tianjin, China: Tianjin Univ. Press, 1995.
42. P. Baldi et al., "Assessing the accuracy of prediction algorithms for classification: An overview, " Bioinformatics, vol. 16, no. 5, pp. 412-424, 2000. (Pubitemid 30487963)
43. K. C. Chou and C. T. Zhang, "Prediction of protein structural classes, " Crit. Rev. Biochem. Mol. Biol., vol. 30, no. 4, pp. 275-349, 1995.
44. K. C. Chou and H. B. Shen, "Cell-PLoc 2. 0: An improved package of web-servers for predicting subcellular localization of proteins in various organisms, " Natural Sci., vol. 2, no. 10, pp. 1090-1103, 2010.
45. K. C. Chou, "Some remarks on protein attribute prediction and pseudo amino acid composition, " J. Theor. Biol., vol. 273, no. 1, pp. 236-247, 2011.
46. T. Huang et al., "Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property, " PLoS One, vol. 6, no. 9, p. E25297, 2011.
47. M. Esmaeili, H. Mohabatkar, and S. Mohsenzadeh, "Using the concept of Chou's pseudo amino acid composition for risk type prediction of human papillomaviruses, " J. Theor. Biol., vol. 263, no. 2, pp. 203-209, 2010.
48. M. Hayat and A. Khan, "Discriminating outer membrane proteins with fuzzy K-nearest neighbor algorithms based on the general form of Chou's PseAAC, " Protein Pept. Lett., vol. 19, no. 4, pp. 411-421, 2012.
49. M. Mohammed Beigi, M. Behjati, and H. Mohabatkar, "Prediction of metalloproteinase family based on the concept of Chou's pseudo amino acid composition using a machine learning approach, " J. Struct. Funct. Genomics, vol. 12, no. 4, pp. 191-197, 2011.
50. K. C. Chou andH. B. Shen, "Plant-mPLoc:A top-down strategy to augment the power for predicting plant protein subcellular localization, " PLoS One, vol. 5, no. 6, p. E11335, 2010.
51. L. M. Zouhal and T. Denoeux, "An evidence-theoretic K-NN rule with parameter optimization, " IEEE Trans. Syst., Man, Cybern., vol. 28, pp. 263-271, 1998. (Pubitemid 128748625)
52. A. L. Boulesteix, "Over-optimism in bioinformatics research, " Bioinformatics, vol. 26, no. 3, pp. 437-439, 2010.
53. A. Pierleoni et al., "BaCelLo: A balanced subcellular localization predictor, " Bioinformatics, vol. 22, no. 14, pp. E408-416, 2006. (Pubitemid 44288310)
54. J. Kyte and R. F. Doolittle, "A simple method for displaying the hydropathic character of a protein, " JMol. Biol., vol. 157, no. 1, pp. 105-132, 1982.
55. K. C. Chou and H. B. Shen, "REVIEW: Recent advances in developing web-servers for predicting protein attributes, " Natural Sci., vol. 1, no. 2, pp. 63-92, 2009.