Protein function prediction with the shortest path in functional linkage graph and boosting

International Journal of Bioinformatics Research and Applications

Volumn 4, Issue 4, 2008, Pages 375-384

  Zhao, Xing Ming ^a,b,c,d   Chen, Luonan ^a,b,d,e   Aihara, Kazuyuki ^b,d  

^a SHANGHAI UNIVERSITY   (China)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c INSTITUTE OF INTELLIGENT MACHINES   (China)

^d INSTITUTE OF INDUSTRIAL SCIENCE   (Japan)

^e OSAKA SANGYO UNIVERSITY   (Japan)

Author keywords

Boosting algorithm; Functional linkage graph; Protein function prediction; Shortest path; Support vector machines

Indexed keywords

ACCURACY; ALGORITHM; ANALYTIC METHOD; ARTICLE; GENE EXPRESSION; GENETIC LINKAGE; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; SUPPORT VECTOR MACHINE;

EID: 55849103231     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2008.021175     Document Type: Article

References (21)

1. Altschul, S., Madden, T., Schafer, A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. (1997) 'Gapped blast and psi-blast: a new generation of protein data', Nucleic Acids Research, Vol. 25, pp.3389-3402.
2. Barutcuoglu, Z., Schapire, R.E. and Troyanskaya, O.G. (2006) 'Hierarchical multi-label prediction of gene function', Bioinformatics, Vol. 22, pp.830-836.
3. Chen, Y. and Xu, D. (2004) 'Global protein function annotation through mining genome-scale data in yeast Saccharomyces', Nucl. Acids Res., Vol. 32, pp.6414-6424.
4. Deng, M., Tu, Z., Sun, F. and Chen, T. (2004) 'Mapping gene ontology to proteins based on protein-protein interaction data', Bioinformatics, Vol. 20, pp.895-902.
5. Dijkstra, E.W. (1959) 'A note on two problems in connexion with graphs', Numerische Mathematik, Vol. 1, pp.269-271.
6. Gavin, A., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J., Michon, A. and Cruciat, C. (2002) 'Functional organization of the yeast proteome by systematic analysis of protein complexes', Nature, Vol. 415, pp.141-147.
7. George, R.A., Spriggs, R.V., Bartlett, G.J., Gutteridge, A., MacArthur, M.W., Porter, C.T., Al-Lazikani, B., Thornton, J.M. and Swindells, M.B. (2005) 'Effective function annotation through catalytic residue conservation', Proc. Natl. Acad. Sci. USA, Vol. 102, pp.12299-12304.
8. Hishigaki, H., Nakai, K., Ono, T., Tanigami, A. and Takagi, T. (2001) 'Assessment of prediction accuracy of protein function from protein-protein interaction data', Yeast, Vol. 18, pp.523-531.
9. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, J.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sørensen, B.D., Matthiesen, J., Hendrickson, R.C., Gleeson, F., Pawson, T., Moran, M.F., Durocher, D., Mann, M., Hogue, C.W., Figeys, D. and Tyers, M. (2002) 'Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry', Nature, Vol. 415, pp.180-183.
10. Hou, J.T., Jun, S.R., Zhang, C. and Kim, S.H. (2005) 'Global mapping of the protein structure space and application in structure-based inference of protein function', Proc. Natl. Acad. Sci. USA, Vol. 102, pp.3651-3656.
11. Hughes, T.R., Marton, M.J., Jones, A.R., Roberts, C.J., Stoughton, R., Armour, C.D., Bennett, H.A., Coffey, E., Dai, H., He, Y.D., Kidd, M.J., King, A.M., Meyer, M.R., Slade, D., Lum, P.Y., Stepaniants, S.B., Shoemaker, D.D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M. and Friend, S.H. (2000) 'Functional discovery via a compendium of expression profiles', Cell, Vol. 102, pp.109-126.
12. Lanckriet, G.R. et al. (2004) 'Kernel-based data fusion and its application to protein function prediction in yeast', Pac. Symp. Biocomput, pp.300-311.
13. Letovsky, S. and Kasif, S. (2003) 'Predicting protein function from protein-protein interaction data: a probabilistic approach', Bioinformatics, Vol. 19, pp.i197-204.
14. Nabieva, E., Jim, K., Agarwal, A., Chazelle, B. and Singh,M.(2005) 'Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps', Bioinformatics, Vol. 21, pp.i302-i310.
15. Pearsom, W. and Lipman, D. (1998) 'Improved tools for biological sequence comparison', Proc. Natl. Acad. Sci. USA, Vol. 85, pp.2444-2448.
16. Polikar, R. (2006) 'Ensemble based systems in decision making', IEEE Circuits and Systems Magazine, Vol. 6, pp.21-45.
17. Ruepp, A., Zollner, A., Maier, D., Albermann, K., Hani, J., Mokrejs, M., Tetko, I., Guldener, U., Mannhaupt, G., Munsterkotter, M. and Mewes, H.W. (2004) 'The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes', Nucl. Acids Res., Vol. 32, pp.5539-5545.
18. Schwikowski, B., Uetz, P. and Fields, S. (2000) 'A network of protein-protein interactions in yeast', Nat. Biotechnol., Vol. 18, pp.1257-1261.
19. Stark, C., Breitkreutz, B.J., Reguly, T., Boucher L., Breitkreutz A. and Tyers, M. (2006) 'BioGRID: A general repository for interaction datasets', Nucleic Acids Res., Vol. 34 (Database issue), pp.D535-D539.
20. Vazquez, A. et al. (2003) 'Global protein function prediction from protein-protein interaction networks', Nat. Biotechnol, Vol. 21, pp.697-670.
21. Zhou, X., Kao, M.J. and Wong, W.H. (2002) 'Transitive functional annotation by shortest-path analysis of gene expression data', PNAS, Vol. 99, pp.12783-12788.