Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4115 LNBI -III, Issue , 2006, Pages 514-524

  Zhang, Shi Hua ^a   Ning, Xue Mei ^a   Liu, Hong Wei ^b   Zhang, Xiang Sun ^a  

^a CHINESE ACADEMY OF SCIENCES   (China)

^b RENMIN UNIVERSITY OF CHINA   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATA REDUCTION; GENETIC ENGINEERING; MEDICAL COMPUTING; YEAST;

MULTIPLE FUNCTIONAL CONSISTENCY; PROTEIN COMPLEXES; PROTEIN PROTEIN INTERACTION (PPI); PROTEIN PROTEIN RELATIONSHIP NETWORK (PPRN);

PROTEINS;

EID: 33749541272     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11816102_55     Document Type: Conference Paper

References (16)

1. Sear, R.P.: Specific Protein-Protein Binding in Many-componet Mixtures of Proteinsn. Phys. Biol., 1(2004), 53-60
2. Bader, G.D., Hogue, C.W.: An Automated Method for Finding Molecular Complexes in Large Protein Interaction Networks. BMC Bioinformatics, 4(2003), 2
3. King, A.D., Pržulj, N., Jurisica, I.: Protein Complex Prediction via Cost-based Clustering. Bioinformatics, 20(2004), 3013-3020
4. Li, X.L., Tan, S.H., Foo, C.S., Ng, S.K.: Interaction Graph Mining for Protein Complexes Using Local Clique Merging. Genome Informatics, 16(2005), 260-269
5. Yamanishi. Y, Vert, J.P., Kanehisa, M.: Protein Network Inference from Multiple Genomic Data: a Supervised Approach. Bioinformatics, 20(2004), i363-i370
6. Lanckriet, G.R., De Bie T.D, Cristianini, N., Jordan, M.I., Noble, W.S.: A Statistical Framework for Genomic Data Fusion. Bioinformatics, 20(2004), 2626-2635
7. Kondor, R.I., Lafferty, J.: Diffusion Kernels on Graphs and Other Discrete Input. In Proceedings of the 19th International Conference on Machine Learning, Morgan Kaufmann, University of South Wales, Sydney, Australia, (2002), 315-322
8. Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S. Sakaki, Y.: Toward a Protein-Protein Interaction Map of the Budding Yeast: a Comprehensive System to Examine Two-hybrid Interactions in Ail Possible Combinations between the Yeast Proteins. Proc. Natl Acad. Sci., USA, 97(2000), 1143-1147
9. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al.: A Comprehensive Analysis of Protein-Protein Interactions in Saccharomyces Cerevisiae. Nature, 403(2000), 623-627
10. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., et al.: Functional Organization of the Yeast Proteome by Systematic Analysis of Protein Complexes. Nature, 415(2002), 141-147
11. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., et al.: Systematic Identification of Protein Complexes in Saccharomyces Cerevisiae by Mass Spectrometry. Nature, 415(2002), 180-183
12. Ruepp, A., Zollner, A., Maier, D., Albermann, K., Hani, J., Mokrejs, M., Tetko, L., Guldener, U., Mannhaupt, G., Munsterkotter, M. et al.: The FunCat, a Functional Annotation Scheme for Systematic Classification of Proteins from Whole Genomes. Nucleic Acids Res., 32(2004), 5539-5545
13. Mewes, H.W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S., Weil, B.: MIPS: a Database for Genomes and Protein Sequences. Nucleic Acids Res. 30(2002), 31-34
14. Barabási, A.-L., Oltvai, Z.N.: Network Biology: Understanding the Cell's Functional Organization. Nature Rev. Genet., 5(2004), 101-114
15. Spirin, V., Mirny, L.A.: Protein Complexes and Functional Modules in Molecular Networks. Proc. Natl Acad. Sci., USA, 100(2003), 12123-12126
16. Segal, E., Wang, H., Koller, D.: Discovering Molecular Pathways from Protein Interaction and Gene Expression Data. Bioinformatics, 19(2003), i264-i272