Prediction of protein subcellular locations using fuzzy k-NN method

Bioinformatics

Volumn 20, Issue 1, 2004, Pages 21-28

  Huang, Ying ^a   Li, Yanda ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; CAENORHABDITIS ELEGANS PROTEIN; DIPEPTIDE; DROSOPHILA PROTEIN; PROTEOME; SACCHAROMYCES CEREVISIAE PROTEIN;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; HUMAN; INFORMATION PROCESSING; MODEL; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; RICE; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS; SWISS-PROT;

ALGORITHMS; ANIMALS; CELLULAR STRUCTURES; DATABASES, PROTEIN; FUZZY LOGIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; PROTEOME; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SPECIES SPECIFICITY; SUBCELLULAR FRACTIONS; TISSUE DISTRIBUTION;

ARABIDOPSIS; ARABIDOPSIS THALIANA; CAENORHABDITIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; MELANOGASTER; ORYZA SATIVA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0347093598     PISSN: 13674803     EISSN: None     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg366     Document Type: Article

References (47)

1. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Bezdek,J.C., Hall,L.O. and Clarke,L.P. (1993) Review of MR image segmentation techniques using pattern recognition. Med. Phys., 20, 1033-1048.
4. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I., Pilbout,S. and Schneider,M. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
5. Cedano,J., Aloy,P., Perez-Pons,J.A. and Querol,E. (1997) Relation between amino acid composition and cellular location of proteins. J. Mol. Biol., 266, 594-600.
6. Cai,Y.D., Liu,X.J., Xu,X.B. and Chou,K.C. (2002) Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect. J. Cell. Biochem., 84, 343-348.
7. Chou,K.C. (1995) A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins Struct. Funct. Genet., 21, 319-344.
8. Chou,K.C. (2000a) Prediction of protein subcellular locations by incorporating quasi-sequence-order effect. Biochem. Biophys. Res. Commun., 278, 477-483.
9. Chou,K.C. (2000b) Review: prediction of protein structural classes and subcellular locations. Curr. Protein Peptide Sci., 1, 171-208.
10. Chou,K.C. (2001) Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins Struct. Funct. Genet., 43, 246-255.
11. Chou,K.C. (2002a) Prediction of protein signal sequences. Curr. Protein Peptide Sci., 3, 615-622.
12. Chou,K.C. (2002b) A new branch of proteomics: prediction of protein cellular attributes. In Weinrer,P.W. and Lu,Q. (eds), Gene Cloning & Expression Technologies, Chapter 4. Eaton Publishing, Westborough, MA, pp. 57-70.
13. Chou,K.C. and Cai,Y.D. (2002) Using functional domain composition and support vector machines for prediction of protein subcellular location. J. Biol. Chem., 277, 45765-45769.
14. Chou,K.C. and Elrod,D.W. (1998) Using discriminant function for prediction of subcellular location of prokaryotic proteins. Biochem. Biophys. Res. Commun., 252, 63-68.
15. Chou,K.C. and Elrod,D.W. (1999a) Protein subcellular location prediction. Protein Eng., 12, 107-118.
16. Chou,K.C. and Elrod,D.W. (1999b) Prediction of membrane protein types and subcellular locations. Proteins Struct. Funct. Genet., 34, 137-153.
17. Chou,K.C. and Zhang,C.T. (1995) Review: prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol., 30, 275-349.
18. Drawid,A. and Gerstein, M. (2000) A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. J. Mol. Biol., 301, 1059-1075.
19. Duda,R.O., Hart,P.E. and Stork,D.G. (2000) Pattern Classification, 2nd edn. Wiley, New York.
20. Emanuelsson,O., Nielsen,H., Brunak,S. and von Heijne,G. (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol., 300, 1005-1016.
21. van Heel,M. (1991) A new family of powerful multivariate statistical sequence analysis techniques. J. Mol. Biol., 220, 877-887.
22. von Heijne,G. (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol., 225, 487-494.
23. Hirokawa,T., Boon-Chieng,S. and Shigeki,M. (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics, 14, 378-379.
24. Hua,S. and Sun,Z. (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics, 17, 721-728.
25. Keller,J.M., Gray,M.R. and Givens,J.A. (1985) A fuzzy k-nearest neighbour algorithm. IEEE Trans. Syst. Man Cybern., 15, 580-585.
26. Krogh,A., Larsson,B., von Heijne,G. and Sonnhammer,E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
27. Kumar,A., Agarwal,S., Heyman,J.A., Matson,S., Heidtman,M., Piccirillo,S., Umansky,L., Drawid,A., Jansen,R., Liu,Y. et al. (2002) Subcellular localization of the yeast proteome. Genes Dev., 16, 707-719.
28. Lio,P. and Vannucci,M. (2000) Wavelet change-point prediction of transmembrane proteins. Bioinformatics, 16, 376-382.
29. Leszczynski,K., Cosby,S., Bissett,R., Provost,D., Boyko,S., Loose,S. and Mvilongo, E. (1999) Application of a fuzzy pattern classifier to decision making in portal verification of radiotherapy. Phys. Med. Biol., 44, 253-269.
30. Mardia,K.V., Kent,J.T. and Bibby,J.M. (1979) Multivariate Analysis. Academic Press, London, pp. 322 and 381.
31. Matthews,B.W. (1975) Comparison of predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
32. Murphy,R.F., Boland,M.V. and Velliste,M. (2000) Towards a systematics for protein subcelluar location: quantitative description of protein localization patterns and automated analysis of fluorescence microscope images. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8, 251-259.
33. Nakai,K. (2000) Protein sorting signals and prediction of subcellular localization. Adv. Protein Chem., 54, 277-344.
34. Nakai,K. and Horton,P. (1999) PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci., 24, 34-36.
35. Nakai,K. and Kanehisa,M. (1991) Expert system for predicting protein localization sites in Gram-negative bacteria. Proteins Struct. Funct. Genet., 11, 95-110.
36. Nakai,K. and Kanehisa,M. (1992) A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics, 14, 897-911.
37. Nakashima,H. and Nishikawa,K. (1994) Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies. J. Mol. Biol., 238, 54-61.
38. Nielsen,H., Engelbrecht,J., Brunak,S. and von Heijne,G. (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng., 10, 1-6.
39. Nielsen,H., Brunak,S. and von Heijne,G. (1999) Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng., 12, 3-9.
40. Reinhardt,A. and Hubbard,T. (1998) Using neural networks for prediction of the subcellular location of proteins. Nucleic Acids Res., 26, 2230-2236.
41. Rost,B., Fariselli,P. and Casadio,R. (1996) Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci., 5, 1704-1718.
42. Yuan,Z. (1999) Prediction of protein subcellular locations using Markov chain models. FEBS Lett., 451, 23-26.
43. Wang,H.C., Dopazo,J., de la Fraga,L.G., Zhu,Y.P. and Carazo,J.M. (1998) Self-organizing tree-growing network for the classification of protein sequences. Protein Sci., 7, 2613-2622.
44. Wu,C., Whitson,G., McLarty,J., Ermongkonchai,A. and Chang,T.C. (1992) Protein classification artificial neural system. Protein Sci., 1, 667-677.
45. Zhang,C.T., Chou,K.C. and Maggiora,G.M. (1995) Predicting protein structural classes from amino acid composition: application of fuzzy clustering. Protein Eng., 8, 425-435.
46. Zhou,G.P. and Assa-Munt,N. (2001) Some insights into protein structural class prediction.Proteins Struct. Funct. Genet., 44, 57-59.
47. Zhou,G.P. and Doctor,K. (2003) Subcellular location prediction of apoptosis proteins. Proteins Struct. Funct. Genet., 50, 44-48.