TESTLoc: Protein subcellular localization prediction from EST data

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Shen, Yao Qing ^a   Burger, Gertraud ^a  

^a Universite de Montreal   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID COMPOSITIONS; CELLULAR COMPARTMENTS; EXPRESSED SEQUENCE TAGS; PHYSICOCHEMICAL PROPERTY; PROTEIN SUBCELLULAR LOCALIZATION PREDICTION; SUBCELLULAR COMPARTMENTS; SUBCELLULAR LOCALIZATIONS; SUBCELLULAR LOCATION OF PROTEINS;

AMINO ACIDS; PEPTIDES; SUPPORT VECTOR MACHINES; TOOLS;

FORECASTING;

EUKARYOTA;

PROTEIN;

ARTICLE; CELL FRACTIONATION; CHEMISTRY; COMPUTER PROGRAM; EXPRESSED SEQUENCE TAG; GENETIC DATABASE; METABOLISM; PROTEIN DATABASE; SEQUENCE ANALYSIS;

DATABASES, GENETIC; DATABASES, PROTEIN; EXPRESSED SEQUENCE TAGS; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; SUBCELLULAR FRACTIONS;

EID: 78149463321     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-563     Document Type: Article

References (58)

1. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK. Global analysis of protein localization in budding yeast. Nature 2003, 425(6959):686-691. 10.1038/nature02026, 14562095.
2. Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, et al. Subcellular localization of the yeast proteome. Genes Dev 2002, 16(6):707-719. 10.1101/gad.970902, 155358, 11914276.
3. Barbe L, Lundberg E, Oksvold P, Stenius A, Lewin E, Bjorling E, Asplund A, Ponten F, Brismar H, Uhlen M, et al. Toward a confocal subcellular atlas of the human proteome. Mol Cell Proteomics 2008, 7(3):499-508.
4. Lascaris R, Bussemaker HJ, Boorsma A, Piper M, van der Spek H, Grivell L, Blom J. Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state. Genome Biol 2003, 4(1):R3. 10.1186/gb-2002-4-1-r3, 151284, 12537548.
5. Yuan HM, Li KL, Ni RJ, Guo WD, Shen Z, Yang CP, Wang BC, Liu GF, Guo CH, Jiang J. A systemic proteomic analysis of Populus chloroplast by using shotgun method. Mol Biol Rep 2010,
6. Li J, Cai T, Wu P, Cui Z, Chen X, Hou J, Xie Z, Xue P, Shi L, Liu P, et al. Proteomic analysis of mitochondria from Caenorhabditis elegans. Proteomics 2009, 9(19):4539-4553. 10.1002/pmic.200900101, 19670372.
7. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
8. Nair R, Rost B. Sequence conserved for subcellular localization. Protein Sci 2002, 11(12):2836-2847. 10.1110/ps.0207402, 2373743, 12441382.
9. Shen YQ, Burger G. Plasticity of a key metabolic pathway in fungi. Funct Integr Genomics 2009, 9(2):145-151. 10.1007/s10142-008-0095-6, 18795352.
10. Shatkay H, Hoglund A, Brady S, Blum T, Donnes P, Kohlbacher O. SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics 2007, 23(11):1410-1417. 10.1093/bioinformatics/btm115, 17392328.
11. Lu Z, Szafron D, Greiner R, Lu P, Wishart DS, Poulin B, Anvik J, Macdonell C, Eisner R. Predicting subcellular localization of proteins using machine-learned classifiers. Bioinformatics 2004, 20(4):547-556. 10.1093/bioinformatics/btg447, 14990451.
12. Nair R, Rost B. Inferring sub-cellular localization through automated lexical analysis. Bioinformatics 2002, 18(Suppl 1):S78-86.
13. Guda C, Subramaniam S. pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics 2005, 21(21):3963-3969. 10.1093/bioinformatics/bti650, 16144808.
14. Scott MS, Thomas DY, Hallett MT. Predicting subcellular localization via protein motif co-occurrence. Genome Res 2004, 14(10A):1957-1966. 10.1101/gr.2650004, 524420, 15466294.
15. Claros MG, Vincens P. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 1996, 241(3):779-786. 10.1111/j.1432-1033.1996.00779.x, 8944766.
16. Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 2000, 300(4):1005-1016. 10.1006/jmbi.2000.3903, 10891285.
17. Bannai H, Tamada Y, Maruyama O, Nakai K, Miyano S. Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 2002, 18(2):298-305. 10.1093/bioinformatics/18.2.298, 11847077.
18. Boden M, Hawkins J. Prediction of subcellular localization using sequence-biased recurrent networks. Bioinformatics 2005, 21(10):2279-2286. 10.1093/bioinformatics/bti372, 15746276.
19. Small I, Peeters N, Legeai F, Lurin C. Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 2004, 4(6):1581-1590. 10.1002/pmic.200300776, 15174128.
20. Reinhardt A, Hubbard T. Using neural networks for prediction of the subcellular location of proteins. Nucleic Acids Res 1998, 26(9):2230-2236. 10.1093/nar/26.9.2230, 147531, 9547285.
21. Hua S, Sun Z. Support vector machine approach for protein subcellular localization prediction. Bioinformatics 2001, 17(8):721-728. 10.1093/bioinformatics/17.8.721, 11524373.
22. Huang Y, Li Y. Prediction of protein subcellular locations using fuzzy k-NN method. Bioinformatics 2004, 20(1):21-28. 10.1093/bioinformatics/btg366, 14693804.
23. Chou KC. Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins 2001, 43(3):246-255. 10.1002/prot.1035, 11288174.
24. Chou KC, Cai YD. Using functional domain composition and support vector machines for prediction of protein subcellular location. J Biol Chem 2002, 277(48):45765-45769. 10.1074/jbc.M204161200, 12186861.
25. Park KJ, Kanehisa M. Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics 2003, 19(13):1656-1663. 10.1093/bioinformatics/btg222, 12967962.
26. Sarda D, Chua GH, Li KB, Krishnan A. pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties. BMC Bioinformatics 2005, 6:152. 10.1186/1471-2105-6-152, 1182350, 15963230.
27. Guda C, Fahy E, Subramaniam S. MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics 2004, 20(11):1785-1794. 10.1093/bioinformatics/bth171, 15037509.
28. Bhasin M, Raghava GP. ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic Acids Res 2004, (32 Web Server):W414-419. 10.1093/nar/gkh350, 441488, 15215421.
29. Nair R, Rost B. Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol 2005, 348(1):85-100. 10.1016/j.jmb.2005.02.025, 15808855.
30. Xie D, Li A, Wang M, Fan Z, Feng H. LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST. Nucleic Acids Res 2005, (33 Web Server):W105-110. 10.1093/nar/gki359, 1160120, 15980436.
31. Yu CS, Lin CJ, Hwang JK. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci 2004, 13(5):1402-1406. 10.1110/ps.03479604, 2286765, 15096640.
32. Blum T, Briesemeister S, Kohlbacher O. MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics 2009, 10(1):274. 10.1186/1471-2105-10-274, 2745392, 19723330.
33. Kaundal R, Saini R, Zhao PX. Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis. Plant Physiol 2010, 154(1):36-54. 10.1104/pp.110.156851, 20647376.
34. Shen YQ, Burger G. 'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools. BMC Bioinformatics 2007, 8:420. 10.1186/1471-2105-8-420, 2176073, 17967180.
35. Liu J, Kang S, Tang C, Ellis LB, Li T. Meta-prediction of protein subcellular localization with reduced voting. Nucleic Acids Res 2007, 35(15):e96. 10.1093/nar/gkm562, 1976432, 17670799.
36. Assfalg J, Gong J, Kriegel HP, Pryakhin A, Wei T, Zimek A. Supervised ensembles of prediction methods for subcellular localization. J Bioinform Comput Biol 2009, 7(2):269-285. 10.1142/S0219720009004072, 19340915.
37. Casadio R, Martelli PL, Pierleoni A. The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation. Brief Funct Genomic Proteomic 2008, 7(1):63-73. 10.1093/bfgp/eln003, 18283051.
38. Briesemeister S, Rahnenfuhrer J, Kohlbacher O. Going from where to why--interpretable prediction of protein subcellular localization. Bioinformatics 2010, 26(9):1232-1238. 10.1093/bioinformatics/btq115, 2859129, 20299325.
39. Pierleoni A, Martelli PL, Fariselli P, Casadio R. BaCelLo: a balanced subcellular localization predictor. Bioinformatics 2006, 22(14):e408-416. 10.1093/bioinformatics/btl222, 16873501.
40. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K. WoLF PSORT: protein localization predictor. Nucleic Acids Res 2007, (35 Web Server):W585-587. 10.1093/nar/gkm259, 1933216, 17517783.
41. Lin HN, Chen CT, Sung TY, Ho SY, Hsu WL. Protein subcellular localization prediction of eukaryotes using a knowledge-based approach. BMC Bioinformatics 2009, 10(Suppl 15):S8. 10.1186/1471-2105-10-S15-S8, 2788359, 19958518.
42. Parkinson J, Blaxter M. Expressed sequence tags: an overview. Methods Mol Biol 2009, 533:1-12. full_text, 19277571.
43. Boguski MS, Lowe TM, Tolstoshev CM. dbEST--database for "expressed sequence tags". Nat Genet 1993, 4(4):332-333. 10.1038/ng0893-332, 8401577.
44. Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan A, Cheung F, Quackenbush J. The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res 2005, (33 Database):D71-74. 540018, 15608288.
45. O'Brien EA, Koski LB, Zhang Y, Yang L, Wang E, Gray MW, Burger G, Lang BF. TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). Nucleic Acids Res 2007, (35 Database):D445-451. 10.1093/nar/gkl770, 1899108, 17202165.
46. Koski LB, Gray MW, Lang BF, Burger G. AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics 2005, 6:151. 10.1186/1471-2105-6-151, 1182349, 15960857.
47. Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S. Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 2008, 320(5878):938-941. 10.1126/science.1157956, 18436743.
48. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2, 10827456.
49. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22(13):1658-1659. 10.1093/bioinformatics/btl158, 16731699.
50. Yu CS, Chen YC, Lu CH, Hwang JK. Prediction of protein subcellular localization. Proteins 2006, 64(3):643-651. 10.1002/prot.21018, 16752418.
51. Devlin TM. The Textbook of Biochemistry. 1992, New York: Wiley-Liss Inc, 3.
52. Fan RE, Chen PH, Lin CJ. Working set selection using the second order information for training SVM. Journal of Machine Learning Research 2005, 6:1889-1918.
53. Wasmuth JD, Blaxter ML. prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics 2004, 5:187. 10.1186/1471-2105-5-187, 543579, 15571632.
54. Iseli C, Jongeneel CV, Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 1999, 138-148.
55. Kanz C, Aldebert P, Althorpe N, Baker W, Baldwin A, Bates K, Browne P, van den Broek A, Castro M, Cochrane G, et al. The EMBL Nucleotide Sequence Database. Nucleic Acids Res 2005, (33 Database):D29-33. 540052, 15608199.
56. Hatzigeorgiou AG, Fiziev P, Reczko M. DIANA-EST: a statistical analysis. Bioinformatics 2001, 17(10):913-919. 10.1093/bioinformatics/17.10.913, 11673235.
57. Chacinska A, Koehler CM, Milenkovic D, Lithgow T, Pfanner N. Importing mitochondrial proteins: machineries and mechanisms. Cell 2009, 138(4):628-644. 10.1016/j.cell.2009.08.005, 19703392.
58. Platta HW, Erdmann R. The peroxisomal protein import machinery. FEBS Lett 2007, 581(15):2811-2819. 10.1016/j.febslet.2007.04.001, 17445803.