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Volumn 98, Issue 2, 2009, Pages 73-79

Predicting protein subnuclear localization using GO-amino-acid composition features

Author keywords

Amino acid composition; Gene Ontology; Subnuclear localization

Indexed keywords

AMINO ACID; BIOINFORMATICS; GENE; PROTEIN;

EID: 70349795723     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2009.06.007     Document Type: Article
Times cited : (28)

References (45)
  • 5
    • 3242877807 scopus 로고    scopus 로고
    • ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST
    • Bhasin M., and Raghava G.P. ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic Acids Res. 32 (2004) W414-W419
    • (2004) Nucleic Acids Res. , vol.32
    • Bhasin, M.1    Raghava, G.P.2
  • 6
    • 4544322645 scopus 로고    scopus 로고
    • Predicting 22 protein localizations in budding yeast
    • Cai Y.D., and Chou K.C. Predicting 22 protein localizations in budding yeast. Biochem. Biophys. Res. Commun. 323 (2004) 425-428
    • (2004) Biochem. Biophys. Res. Commun. , vol.323 , pp. 425-428
    • Cai, Y.D.1    Chou, K.C.2
  • 7
    • 13844280973 scopus 로고    scopus 로고
    • Predicting enzyme family classes by hybridizing gene product composition and pseudo-amino acid composition
    • Cai Y.D., Zhou G.P., and Chou K.C. Predicting enzyme family classes by hybridizing gene product composition and pseudo-amino acid composition. J. Theor. Biol. 234 (2005) 145-149
    • (2005) J. Theor. Biol. , vol.234 , pp. 145-149
    • Cai, Y.D.1    Zhou, G.P.2    Chou, K.C.3
  • 8
    • 33747856187 scopus 로고    scopus 로고
    • Protein classification using probabilistic chain graphs and the Gene Ontology structure
    • Carroll S., and Pavlovic V. Protein classification using probabilistic chain graphs and the Gene Ontology structure. Bioinformatics 22 (2006) 1871-1878
    • (2006) Bioinformatics , vol.22 , pp. 1871-1878
    • Carroll, S.1    Pavlovic, V.2
  • 9
    • 0031588694 scopus 로고    scopus 로고
    • Relation between amino acid composition and cellular location of proteins
    • Cedano J., Aloy P., Perez-Pons J.A., and Querol E. Relation between amino acid composition and cellular location of proteins. J. Mol. Biol. 266 (1997) 594-600
    • (1997) J. Mol. Biol. , vol.266 , pp. 594-600
    • Cedano, J.1    Aloy, P.2    Perez-Pons, J.A.3    Querol, E.4
  • 11
    • 33745759451 scopus 로고    scopus 로고
    • Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization
    • Chou K.C., and Shen H.B. Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization. Biochem. Biophys. Res. Commun. 347 (2006) 150-157
    • (2006) Biochem. Biophys. Res. Commun. , vol.347 , pp. 150-157
    • Chou, K.C.1    Shen, H.B.2
  • 12
    • 34249318001 scopus 로고    scopus 로고
    • Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites
    • Chou K.C., and Shen H.B. Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. J. Proteome Res. 6 (2007) 1728-1734
    • (2007) J. Proteome Res. , vol.6 , pp. 1728-1734
    • Chou, K.C.1    Shen, H.B.2
  • 13
    • 34548606295 scopus 로고    scopus 로고
    • Recent progress in protein subcellular location prediction
    • Chou K.C., and Shen H.B. Recent progress in protein subcellular location prediction. Anal. Biochem. 370 (2007) 1-16
    • (2007) Anal. Biochem. , vol.370 , pp. 1-16
    • Chou, K.C.1    Shen, H.B.2
  • 14
    • 39449105071 scopus 로고    scopus 로고
    • Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms
    • Chou K.C., and Shen H.B. Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nat. Protoc. 3 (2008) 153-162
    • (2008) Nat. Protoc. , vol.3 , pp. 153-162
    • Chou, K.C.1    Shen, H.B.2
  • 15
    • 33747197197 scopus 로고    scopus 로고
    • Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-nearest neighbor classifiers
    • Chou K.C., and Shen H.B. Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-nearest neighbor classifiers. J. Proteome Res. 5 (2006) 1888-1897
    • (2006) J. Proteome Res. , vol.5 , pp. 1888-1897
    • Chou, K.C.1    Shen, H.B.2
  • 17
    • 9644278424 scopus 로고    scopus 로고
    • Significance of subnuclear localization of key players of inositol lipid cycle
    • Cocco L., Manzoli L., Barnabei O., and Martelli A.M. Significance of subnuclear localization of key players of inositol lipid cycle. Adv. Enzyme Regul. 44 (2004) 51-60
    • (2004) Adv. Enzyme Regul. , vol.44 , pp. 51-60
    • Cocco, L.1    Manzoli, L.2    Barnabei, O.3    Martelli, A.M.4
  • 19
    • 0742290016 scopus 로고    scopus 로고
    • Inheritable genetic algorithm for biobjective 0/1 combinatorial optimization problems and its applications
    • Ho S.Y., Chen J.H., and Huang M.H. Inheritable genetic algorithm for biobjective 0/1 combinatorial optimization problems and its applications. IEEE Trans. Syst. Man Cyb., Part B 34 (2004) 609-620
    • (2004) IEEE Trans. Syst. Man Cyb., Part B , vol.34 , pp. 609-620
    • Ho, S.Y.1    Chen, J.H.2    Huang, M.H.3
  • 20
    • 33747067136 scopus 로고    scopus 로고
    • Interpretable gene expression classifier with an accurate and compact fuzzy rule base for microarray data analysis
    • Ho S.Y., Hsieh C.H., Chen H.M., and Huang H.L. Interpretable gene expression classifier with an accurate and compact fuzzy rule base for microarray data analysis. BioSystems 85 (2006) 165-176
    • (2006) BioSystems , vol.85 , pp. 165-176
    • Ho, S.Y.1    Hsieh, C.H.2    Chen, H.M.3    Huang, H.L.4
  • 21
    • 11844263947 scopus 로고    scopus 로고
    • Intelligent evolutionary algorithms for large parameter optimization problems
    • Ho S.Y., Shu L.S., and Chen J.H. Intelligent evolutionary algorithms for large parameter optimization problems. IEEE Trans. Evolut. Comput. 8 (2004) 522-541
    • (2004) IEEE Trans. Evolut. Comput. , vol.8 , pp. 522-541
    • Ho, S.Y.1    Shu, L.S.2    Chen, J.H.3
  • 22
    • 0034843744 scopus 로고    scopus 로고
    • Support vector machine approach for protein subcellular localization prediction
    • Hua S., and Sun Z. Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17 (2001) 721-728
    • (2001) Bioinformatics , vol.17 , pp. 721-728
    • Hua, S.1    Sun, Z.2
  • 23
    • 34548425686 scopus 로고    scopus 로고
    • Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method
    • Huang W.L., Chen H.M., Hwang S.F., and Ho S.Y. Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method. BioSystems 90 (2007) 405-418
    • (2007) BioSystems , vol.90 , pp. 405-418
    • Huang, W.L.1    Chen, H.M.2    Hwang, S.F.3    Ho, S.Y.4
  • 24
    • 40249110012 scopus 로고    scopus 로고
    • ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization
    • Huang W.L., Tung C.W., Ho S.W., Hwang S.F., and Ho S.Y. ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC Bioinformatics 9 (2008) 80
    • (2008) BMC Bioinformatics , vol.9 , pp. 80
    • Huang, W.L.1    Tung, C.W.2    Ho, S.W.3    Hwang, S.F.4    Ho, S.Y.5
  • 25
    • 34548458988 scopus 로고    scopus 로고
    • ProLoc: Prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features
    • Huang W.L., Tung C.W., Huang H.L., Hwang S.F., and Ho S.Y. ProLoc: Prediction of protein subnuclear localization using SVM with automatic selection from physicochemical composition features. BioSystems 90 (2007) 573-581
    • (2007) BioSystems , vol.90 , pp. 573-581
    • Huang, W.L.1    Tung, C.W.2    Huang, H.L.3    Hwang, S.F.4    Ho, S.Y.5
  • 26
    • 33751393465 scopus 로고    scopus 로고
    • Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction
    • Lei Z., and Dai Y. Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction. BMC Bioinformatics (2006) 491-590
    • (2006) BMC Bioinformatics , pp. 491-590
    • Lei, Z.1    Dai, Y.2
  • 27
    • 33750580714 scopus 로고    scopus 로고
    • Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data
    • Lewin A., and Grieve I. Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data. BMC Bioinformatics 7 (2006) 426
    • (2006) BMC Bioinformatics , vol.7 , pp. 426
    • Lewin, A.1    Grieve, I.2
  • 28
    • 33749628461 scopus 로고    scopus 로고
    • Identification and analysis of the mouse basic/Helix-Loop-Helix transcription factor family
    • Li J., Liu Q., Qiu M., Pan Y., Li Y., and Shi T. Identification and analysis of the mouse basic/Helix-Loop-Helix transcription factor family. Biochem. Biophys. Res. Commun. 350 (2006) 648-656
    • (2006) Biochem. Biophys. Res. Commun. , vol.350 , pp. 648-656
    • Li, J.1    Liu, Q.2    Qiu, M.3    Pan, Y.4    Li, Y.5    Shi, T.6
  • 29
    • 7244248755 scopus 로고    scopus 로고
    • A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression
    • Li T., Zhang C., and Ogihara M. A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression. Bioinformatics 20 (2004) 2429-2437
    • (2004) Bioinformatics , vol.20 , pp. 2429-2437
    • Li, T.1    Zhang, C.2    Ogihara, M.3
  • 30
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews B.W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta 405 (1975) 442-451
    • (1975) Biochim. Biophys. Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 31
    • 16244398103 scopus 로고    scopus 로고
    • Mimicking cellular sorting improves prediction of subcellular localization
    • Nair R., and Rost B. Mimicking cellular sorting improves prediction of subcellular localization. J. Mol. Biol. 348 (2005) 85-100
    • (2005) J. Mol. Biol. , vol.348 , pp. 85-100
    • Nair, R.1    Rost, B.2
  • 32
    • 33646871614 scopus 로고    scopus 로고
    • An ensemble of K-local hyperplanes for predicting protein-protein interactions
    • Nanni L., and Lumini A. An ensemble of K-local hyperplanes for predicting protein-protein interactions. Bioinformatics 22 (2006) 1207-1210
    • (2006) Bioinformatics , vol.22 , pp. 1207-1210
    • Nanni, L.1    Lumini, A.2
  • 34
    • 33747195620 scopus 로고    scopus 로고
    • A novel computational method to predict transcription factor DNA binding preference
    • Qian Z., Cai Y.D., and Li Y. A novel computational method to predict transcription factor DNA binding preference. Biochem. Biophys. Res. Commun. 348 (2006) 1034-1037
    • (2006) Biochem. Biophys. Res. Commun. , vol.348 , pp. 1034-1037
    • Qian, Z.1    Cai, Y.D.2    Li, Y.3
  • 35
    • 85194545017 scopus 로고    scopus 로고
    • Quinlan, J.R., 2003. C5.0 Online Tutorial. http://www.rulequest.com.
    • Quinlan, J.R., 2003. C5.0 Online Tutorial. http://www.rulequest.com.
  • 36
    • 25444506574 scopus 로고    scopus 로고
    • pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties
    • Sarda D., Chua G.H., Li K.B., and Krishnan A. pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties. BMC Bioinformatics 6 (2005) 152
    • (2005) BMC Bioinformatics , vol.6 , pp. 152
    • Sarda, D.1    Chua, G.H.2    Li, K.B.3    Krishnan, A.4
  • 37
    • 26844455291 scopus 로고    scopus 로고
    • Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition
    • Shen H.B., and Chou K.C. Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition. Biochem. Biophys. Res. Commun. 337 (2005) 752-756
    • (2005) Biochem. Biophys. Res. Commun. , vol.337 , pp. 752-756
    • Shen, H.B.1    Chou, K.C.2
  • 38
    • 33847668306 scopus 로고    scopus 로고
    • Hum-mPLoc: An ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites
    • Shen H.B., and Chou K.C. Hum-mPLoc: An ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites. Biochem. Biophys. Res. Commun. 355 (2007) 1006-1011
    • (2007) Biochem. Biophys. Res. Commun. , vol.355 , pp. 1006-1011
    • Shen, H.B.1    Chou, K.C.2
  • 39
    • 36448952353 scopus 로고    scopus 로고
    • Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM. Protein Engineering
    • Shen H.B., and Chou K.C. Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM. Protein Engineering. Des. Select. 20 (2007) 561-567
    • (2007) Des. Select. , vol.20 , pp. 561-567
    • Shen, H.B.1    Chou, K.C.2
  • 40
    • 0000629975 scopus 로고
    • Cross-validatory choice and assessment of statistical predictions
    • Stone M. Cross-validatory choice and assessment of statistical predictions. J. Roy. Stat. Soc. 36 (1974) 111-147
    • (1974) J. Roy. Stat. Soc. , vol.36 , pp. 111-147
    • Stone, M.1
  • 41
    • 34249687092 scopus 로고    scopus 로고
    • POPI: Predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties
    • Tung C.W., and Ho S.Y. POPI: Predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties. Bioinformatics 23 (2007) 942-949
    • (2007) Bioinformatics , vol.23 , pp. 942-949
    • Tung, C.W.1    Ho, S.Y.2
  • 43
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang G.L., and Dunbrack Jr. R.L. PISCES: a protein sequence culling server. Bioinformatics 19 (2003) 1589-1591
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.L.1    Dunbrack Jr., R.L.2
  • 45
    • 33746218840 scopus 로고    scopus 로고
    • Prediction of protein subcellular localization
    • Yu C.S., Chen Y.C., Lu C.H., and Hwang J.K. Prediction of protein subcellular localization. Proteins 64 (2006) 643-651
    • (2006) Proteins , vol.64 , pp. 643-651
    • Yu, C.S.1    Chen, Y.C.2    Lu, C.H.3    Hwang, J.K.4


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