CombFunc: Predicting protein function using heterogeneous data sources

Nucleic Acids Research

Volumn 40, Issue W1, 2012, Pages

  Wass, Mark N ^a,b   Barton, Geraint ^a   Sternberg, Michael J E ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b Centro Nacional de Investigaciones Oncológicas   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CLIENT SERVER APPLICATION; COMPUTER PROGRAM; GENE EXPRESSION; GENETIC CONSERVATION; INTERMETHOD COMPARISON; MOLECULAR BIOLOGY; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; QUALITY CONTROL; SUPPORT VECTOR MACHINE; WEB BROWSER;

ALGORITHMS; GENE EXPRESSION; INTERNET; PROTEIN INTERACTION MAPS; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84864437522     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks489     Document Type: Article

References (43)

1. Erdin, S., Lisewski, A.M. and Lichtarge, O. (2011) Protein function prediction: towards integration of similarity metrics. Curr. Opin. Struct. Biol., 21, 180-188.
2. 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.
3. Devos, D. and Valencia, A. (2000) Practical limits of function prediction. Proteins, 41, 98-107.
4. Martin, D.M., Berriman, M. and Barton, G.J. (2004) GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC bioinformatics, 5, 178.
5. Hawkins, T., Chitale, M., Luban, S. and Kihara, D. (2009) PFP: automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins, 74, 566-582.
6. Chitale, M., Hawkins, T., Park, C. and Kihara, D. (2009) ESG: extended similarity group method for automated protein function prediction. Bioinformatics, 25, 1739-1745.
7. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T. et al. (2000) Gene ontology: tool for the unification of biology. the gene ontology consortium. Nat. Genet., 25, 25-29.
8. Clark, W.T. and Radivojac, P. (2011) Analysis of protein function and its prediction from amino acid sequence. Proteins, 79, 2086-2096.
9. Engelhardt, B.E., Jordan, M.I., Srouji, J.R. and Brenner, S.E. (2011) Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res., 21, 1969-1980.
10. Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res., 40, D306-D312.
11. Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J. et al. (2012) The pfam protein families database. Nucleic Acids Res., 40, D290-D301.
12. Dimmer, E.C., Huntley, R.P., Alam-Faruque, Y., Sawford, T., O'Donovan, C., Martin, M.J., Bely, B., Browne, P., Mun Chan, W., Eberhardt, R. et al. (2012) The UniProt-GO annotation database in 2011. Nucleic Acids Res., 40, D565-D570.
13. Forslund, K. and Sonnhammer, E.L. (2008) Predicting protein function from doma in content. Bioinformatics, 24, 1681-1687.
14. Wass, M.N. and Sternberg, M.J. (2008) ConFunc-functional annotation in the twilight zone. Bioinformatics, 24, 798-806.
15. Chua, H.N., Sung, W.K. and Wong, L. (2006) Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics, 22, 1623-1630.
16. Vazquez, A., Flammini, A., Maritan, A. and Vespignani, A. (2003) Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol., 21, 697-700.
17. Brown, M.P., Grundy, W.N., Lin, D., Cristianini, N., Sugnet, C.W., Furey, T.S., Ares, M. Jr and Haussler, D. (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci. USA, 97, 262-267.
18. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
19. Lobley, A., Swindells, M.B., Orengo, C.A. and Jones, D.T. (2007) Inferring function using patterns of native disorder in proteins. PLoS Computat. Biol., 3, e162.
20. Laskowski, R.A., Watson, J.D. and Thornton, J.M. (2005) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res., 33, W89-W93.
21. Pal, D. and Eisenberg, D. (2005) Inference of protein function from protein structure. Structure London, 13, 121-130.
22. Zhang, Q.C., Deng, L., Fisher, M., Guan, J., Honig, B. and Petrey, D. (2011) PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res., 39, W283-W287.
23. Guan, Y., Myers, C.L., Hess, D.C., Barutcuoglu, Z., Caudy, A.A. and Troyanskaya, O.G. (2008) Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biol., 9(Suppl. 1), S3.
24. Troyanskaya, O.G., Dolinski, K., Owen, A.B., Altman, R.B. and Botstein, D. (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc. Natl Acad. Sci. USA, 100, 8348-8353.
25. Obozinski, G., Lanckriet, G., Grant, C., Jordan, M.I. and Noble, W.S. (2008) Consistent probabilistic outputs for protein function prediction. Genome Biol., 9(Suppl. 1), S6.
26. Nariai, N., Kolaczyk, E.D. and Kasif, S. (2007) Probabilistic protein function prediction from heterogeneous genome-wide data. PloS One, 2, e337.
27. Gherardini, P.F. and Helmer-Citterich, M. (2008) Structure-based function prediction: approaches and applications. Brief. Funct. Genom Proteomics, 7, 291-302.
28. Wass, M.N., Stanway, R., Blagborough, A.M., Lal, K., Prieto, J.H., Raine, D., Sternberg, M.J., Talman, A.M., Tomley, F., Yates, J. et al. (2012) Proteomic analysis of Plasmodium in the mosquito: progress and pitfalls. Parasitology, February 16 (doi:10.1017/S0031182012000133; epub ahead of print).
29. 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.
30. Kerrien, S., Aranda, B., Breuza, L., Bridge, A., Broackes-Carter, F., Chen, C., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U. et al. (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res., 40, D841-D846.
31. Licata, L., Briganti, L., Peluso, D., Perfetto, L., Iannuccelli, M., Galeota, E., Sacco, F., Palma, A., Nardozza, A.P., Santonico, E. et al. (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res., 40, D857-D861.
32. Obayashi, T. and Kinoshita, K. (2011) COXPRESDB: a database to compare gene coexpression in seven model animals. Nucleic Acids Res., 39, D1016-D1022.
33. Vapnik, V.N. (1999) An overview of statistical learning theory. IEEE Transact Neural Networks/a publication of the IEEE Neural Networks Council, 10, 988-999.
34. Kelley, L.A. and Sternberg, M.J. (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protocols, 4, 363-371.
35. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res, 39, D214-D219.
36. Chubb, D., Jefferys, B.R., Sternberg, M.J. and Kelley, L.A. (2010) Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe. Bioinformatics, 26, 2664-2671.
37. Soding, J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
38. Schwikowski, B., Uetz, P. and Fields, S. (2000) A network of protein-protein interactions in yeast. Nat. Biotechnol., 18, 1257-1261.
39. Obayashi, T., Hayashi, S., Shibaoka, M., Saeki, M., Ohta, H. and Kinoshita, K. (2008) COXPRESDB: a database of coexpressed gene networks in mammals. Nucleic Acids Res., 36, D77-82.
40. Platt, J.C. (1999) Advances in Large Margin Classifiers, Vol. 1. MIT Press, Cambridge, Massachusetts, US, pp. 61-74.
41. Huang, Y., Niu, B., Gao, Y., Fu, L. and Li, W. (2010) CD-HIT suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26, 680-682.
42. Wass, M.N., Kelley, L.A. and Sternberg, M.J. (2010) 3DLigandSite: predicting liganD-binding sites using similar structures. Nucleic Acids Res., 38, W469-W473.
43. Wass, M.N. and Sternberg, M.J. (2009) Prediction of ligand binding sites using homologous structures and conservation at CASP8. Proteins, 77(Suppl. 9), 147-151.