YLoc-an interpretable web server for predicting subcellular localization

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Briesemeister, Sebastian ^a   Rahnenführer, Jörg ^b   Kohlbacher, Oliver ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b TU DORTMUND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CELL MEMBRANE; CELLULAR DISTRIBUTION; COMPUTER INTERFACE; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; ENDOPLASMIC RETICULUM; PRIORITY JOURNAL; PROBABILITY; PROTEIN ENGINEERING; PROTEIN LOCALIZATION; RELIABILITY; WEB BROWSER; ANIMAL; CELL ORGANELLE; CHEMISTRY; INTERNET; REPRODUCIBILITY; SEQUENCE ANALYSIS;

ANIMALS; FUNGAL PROTEINS; INTERNET; ORGANELLES; PLANT PROTEINS; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

FUNGAL PROTEIN; PROTEIN; VEGETABLE PROTEIN;

EID: 77954274687     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq477     Document Type: Article

References (29)

1. Nakai,K. and Kanehisa,M. (1992) A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics, 14, 897-911.
2. Horton,P. and Nakai,K. (1997) Better prediction of protein cellular localization sites with the k nearest neighbor classifier. Intell. Syst. Mol. Biol., 5, 147-152.
3. Chou,K. and Cai,Y. (2003) Prediction and classification of protein subcellular location-sequence-order effect and pseudo amino acid composition. J. Cell. Biochem., 90, 1250-1260.
4. Nair,R. and Rost,B. (2005) Mimicking cellular sorting improves prediction of subcellular localization. J. Mol. Biol., 348, 85-100.
5. Petsalaki,E., Bagos,P., Litou,Z. and Hamodrakas,S. (2006) PredSL: a tool for the N-terminal sequence-based prediction of protein subcellular localization. Genomics Proteomics Bioinformatics, 4, 48-55.
6. Pierleoni,A., Martelli,P., Fariselli,P. and Casadio,R. (2006) BaCelLo: a balanced subcellular localization predictor. Bioinformatics, 22, e408-e416.
7. Höglund,A., Dönnes,P., Blum,T., Adolph,H. and Kohlbacher,O. (2006) MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinformatics, 22, 1158-1165.
8. Emanuelsson,O., Brunak,S., von Heijne,G. and Nielsen,H. (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc., 2, 953-971.
9. Horton,P., Park,K., Obayashi,T., Fujita,N., Harada,H., Adams-Collier,C. and Nakai,K. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res.., 35, W585-W587.
10. Chou,K. and Cai,Y. (2002) Using functional domain composition and support vector machines for prediction of protein subcellular location. J. Biol. Chem., 277, 45765-45769.
11. Scott,M., Thomas,D. and Hallett,M. (2004) Predicting subcellular localization via protein motif co-occurrence. Genome Res., 14, 1957-1966.
12. Garg,A. and Raghava,G. (2008) ESLpred 2: improved method for predicting subcellular localization of eukaryotic proteins. BMC Bioinformatics, 9, 503.
13. Lin,H.N., Chen,C.T., Sung,T.Y., Ho,S.Y. and Hsu,W.L. (2009) Protein subcellular localization prediction of eukaryotes using a knowledge-based approach. BMC Bioinformatics, 10, S8.
14. Huang,W., Tung,C., Ho,S., Hwang,S. and Ho,S. (2008) ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC Bioinformatics, 9, 80.
15. Brady,S. and Shatkay,H. (2008) EpiLoc: a (working) text-based system for predicting protein subcellular location. Pacific Symposium on Biocomputing. World Scientific, pp. 604-615.
16. Fyshe,A., Liu,Y., Szafron,D., Greiner,R. and Lu,P. (2008) Improving subcellular localization prediction using text classification and the Gene Ontology. Bioinformatics, 24, 2512-2517.
17. Chou,K. and Cai,Y. (2003) A new hybrid approach to predict subcellular localization of proteins by incorporating Gene Ontology. Biochem. Biophys. Res. Commun., 311, 743-747.
18. Scott,M., Calafell,S., Thomas,D. and Hallett,M. (2005) Refining protein subcellular localization. PLoS Comput. Biol., 1, e66.
19. Chou,K. and Shen,H. (2007) Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. J. Proteome Res., 6, 1728-1734.
20. Blum,T., Briesemeister,S. and Kohlbacher,O. (2009) MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics, 10, 274.
21. Briesemeister,S., Blum,T., Brady,S., Lam,Y., Kohlbacher,O. and Shatkay,H. (2009) SherLoc2: a high-accuracy hybrid method for predicting protein subcellular localization. J. Proteome Res., 8, 5363-5366.
22. Zhang,S., Xia,X., Shen,J., Zhou,Y. and Sun,Z. (2008) DBMLoc: a database of proteins with multiple subcellular localizations. BMC Bioinformatics, 9, 127.
23. Hall,M. (2000) Correlation-based feature selection for discrete and numeric class machine learning. Proceedings of the Seventeenth International Conference on Machine Learning. Morgan Kaufman Publishers, pp. 359-366.
24. Whitten,I. and Frank,E. (2005) Data Mining: Practical Machine Learning Tools and Techniques. Morgan Kaufman Publishers, San Fransisco, CA.
25. Fayyad,U.M. and Irani,K. (1993) Multi-interval discretization of continuous-valued attributes for classification learning. Proceedings of the 13th International Joint Conference on Artificial Intelligence. Morgan Kaufmann Publishers, pp. 1022-1027.
26. Briesemeister,S., Rahnenführer,J. and Kohlbacher,O. (2010) Going from where to why - interpretable prediction of protein subcellular localization. Bioinformatics, 26, 1232-1238.
27. Casadio,R., Martelli,P. and Pierleoni,A. (2008) The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation. Brief. Funct. Genomic Proteomic, 7, 63-67.
28. Tsoumakas,G. and Katakis,I. (2007) Multi-label classification: an overview. Int. J. Data Warehousing Min., 3, 1-13.
29. Tolley,E. and Craig,I. (1975) Presence of two forms of fumarase (fumarate hydratase E.C. 4.2.1.2) in mammalian cells: immunological characterization and genetic analysis in somatic cell hybrids. Confirmation of the assignment of a gene necessary for the enzyme expression to human chromosome 1. Biochem. Genet., 13, 867-883.