Prelocabc: A novel predictor of protein sub-cellular localization using a Bayesian classifier

Journal of Proteomics and Bioinformatics

Volumn 4, Issue 2, 2011, Pages 44-52

  Zhang, Yanqiong ^a   Li, Tao ^a   Yang, Chunyuan ^a   Li, Dong ^a   Cui, Yu ^a   Jiang, Ying ^a   Zhang, Lingqiang ^a   Zhu, Yunping ^a   He, Fuchu ^a  

^a BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

Author keywords

Bayesian model; Bioinformatics; Classifier; Sub cellular localization

Indexed keywords

AMINO ACID COMPOSITION; ARTICLE; BAYES THEOREM; CELL SELECTION; CELLULAR DISTRIBUTION; CLASSIFICATION ALGORITHM; CONTROLLED STUDY; HUMAN; MASS SPECTROMETRY; MATHEMATICAL MODEL; NONHUMAN; ONLINE SYSTEM; PREDICTION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MOTIF; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; STRUCTURAL HOMOLOGY;

EID: 79952148058     PISSN: None     EISSN: 0974276X     Source Type: Journal    
DOI: 10.4172/jpb.1000165     Document Type: Article

References (43)

1. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425: 686-691.
2. Andersen JS, Wilkinson CJ, Mayor T, Mortensen P, Nigg EA, et al. (2003) Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426: 570-574.
3. Kislinger T, Cox B, Kannan A, Chung C, Hu P, et al. (2006) Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125: 173-186.
4. Ying W, Jiang Y, Guo L, Hao Y, Zhang Y, et al. (2006) A dataset of human fetal liver proteome identified by sub-cellular fractionation and multiple protein separation and identification technology. Mol cell proteomics 5: 1703-1707.
5. Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, et al. (2006) A mammalian organelle map by protein correlation profiling. Cell 125: 187-199.
6. Nielsen H, Engelbrecht J, Brunak S, Heijne G (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10: 1-6.
7. Claros MG, Vincens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J biochem 241: 779-786.
8. Emanuelsson O, Nielsen H, Brunak S, Heijne G (2000) Predicting sub-cellular localization of proteins based on their N-terminal amino acid sequence. J mol biol 300: 1005-1016.
9. 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.
10. Hawkins J, Davis L, Bodén M (2007) Predicting nuclear localization. J Proteome Res 6: 1402-1409.
11. Nakai K, Kanehisa M (1992) A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14: 897-911.
12. Guda C, Fahy E, Subramaniam S (2004) MITOPRED: A genome-scale method for prediction of nuclear-encoded mitochondrial proteins. Bioinformatics 20: 1785-1794
13. Guda C, Subramaniam S (2005) pTARGET a new method for predicting protein sub-cellular localization in eukaryotes. Bioinformatics 21: 3963-3969.
14. Fyshe A, Liu Y, Szafron D, Greiner R, Lu P (2008) Improving subcellular localization prediction using text classification and the gene ontology. Bioinformatics 24: 2512-2517.
15. Lee K, Chuang HY, Beyer A, Sung MK, Huh WK, et al. (2008) Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res 36: e136.
16. Shin CJ, Wong S, Davis MJ, Ragan MA (2009) Protein-protein interaction as a predictor of subcellular location. BMC Syst Biol 25: 3-28.
17. Marcotte EM, Xenarios I, van Der Bliek AM, Eisenberg D (2000) Localizing proteins in the cell from their phylogenetic profiles. Proc Natl Acad Sci U S A 97: 12115-12120.
18. Szafron D, Lu P, Greiner R, Wishart DS, Poulin B et al. (2004) Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. Nucleic Acids Res 32: W365-W371
19. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31: 365-370
20. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
21. Du P, Li Y (2006) Prediction of protein submitochondria locations by hybridizing pseudo-amino acid composition with various physicochemical features of segmented sequence. BMC Bioinformatics 7: 518.
22. Scott M, Lu G, Hallett M, Thomas DY (2004) The Hera database and its use in the characterization of endoplasmic reticulum proteins. Bioinformatics 20: 937-944.
23. Fink JL, Aturaliya RN, Davis MJ, Zhang F, Hanson K (2006) LOCATE: a mouse protein sub-cellular localization database. Nucleic Acids Res 34: 213-217
24. Höglund A, Dönnes P, Blum T, Adolph HW, Kohlbacher O (2006) MultiLoc: prediction of protein sub-cellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinformatics 22: 1158-1165.
25. Horton P, Park KJ, Obayashi T, Fujita N, Harada H et al. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35: W585-W587.
26. Stone M (1974) Cross-validatory choice and assessment of statistical predictions. J Royal Stat Soc 36: 111-147.
27. Matthew BW (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 405: 442-451.
28. Huang Y, Li YD (2004) Prediction of protein sub-cellular localizations using fuzzy k-NN method. Bioinform 20: 21-28.
29. Ludbrook J (2008) Analysis of 2 x 2 tables of frequencies: matching test to experimental design. Int J Epidemiol 37: 1430-1435.
30. Huang WL, Tung CW, Ho SW, Hwang SF, Ho SY (2008) ProLoc-GO: utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC Bioinformatics 9: 80.
31. Habib T, Zhang C, Yang JY, Yang MQ, Deng Y (2008) Supervised learning method for the prediction of sub-cellular localization of proteins using amino acid and amino acid pair composition. BMC Genomics 9: S16.
32. Liu J, Kang S, Tang C, Ellis LB, Li T (2007) Meta-prediction of protein subcellular localization with reduced voting. Nucleic Acids Res 35: e96.
33. Shen YQ, Burger G (2007) 'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools. BMC Bioinformatics 8: 420.
34. Sprenger J, Fink JL, Teasdale RD (2006) Evaluation and comparison of mammalian sub-cellular localization prediction methods. BMC Bioinformatics 7: S3.
35. Scott MS, Calafell SJ, Thomas DY, Hallett MT (2005) Refining protein sub-cellular localization. PLoS comput boil 1: e66.
36. Chou KC, Shen HB (2008) Cell-PLoc: a package of Web servers for predicting sub-cellular localization of proteins in various organisms. Nat protoc 3: 153-162.
37. Yates JR, Gilchrist A, Howell KE, Bergeron JJ (2005) Proteomics of organelles and large cellular structures. Nat Rev Mol cell Biol 6: 702-714.
38. Andersen JS, Mann M (2006) Organellar proteomics: turning inventories into insights. EMBO reports 7: 874-879.
39. Tantoso E, Li KB (2008) AAIndexLoc: predicting subcellular localization of proteins based on a new representation of sequences using amino acid indices. Amino Acids 35: 345-53.
40. Briesemeister S, Rahnenführer J, Kohlbacher O (2010) Going from where to why - interpretable prediction of protein subcellular localization. Bioinformatics 26: 1232-1238.
41. Nasibov E, Kandemir-Cavas C (2008) Protein subcellular location prediction using optimally weighted fuzzy k-NN algorithm. Comput Biol Chem 32: 448-51.
42. Petsalaki EI, Bagos PG, Litou ZI, Hamodrakas SJ (2006) PredSL: a tool for the N-terminal sequence-based prediction of protein subcellular localization. Genomics Proteomics Bioinformatics 4: 48-55.
43. 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.