Inferring domain-domain interactions from protein-protein interactions

Genome Research

Volumn 12, Issue 10, 2002, Pages 1540-1548

  Deng, Minghua ^a   Mehta, Shipra ^a   Sun, Fengzhu ^a   Chen, Ting ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTICAL ERROR; ARTICLE; CONTROLLED STUDY; CORRELATION COEFFICIENT; DATA ANALYSIS; GENE EXPRESSION PROFILING; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; RANDOMIZATION; SACCHAROMYCES CEREVISIAE; SEQUENCE DATABASE; TWO HYBRID SYSTEM;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; LIKELIHOOD FUNCTIONS; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0036799752     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.153002     Document Type: Article

References (26)

1. Bairoch, A. and Apweiler, R. 2000. The SWISSPROT protein sequence database and its supplement TrEMBL, in 2000. Nucleic Acids Res. 28: 45-48.
2. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S., Griffiths-Jones, S., Howe, K., Marshall, M., and Sonnhammer, E. 2002. The PFAM Protein Families Database Nucleic Acids Res. 30: 276-280.
3. Bock, J.R. and Gough, D.A.. 2001. Predicting protein-protein interactions from primary structure. Bioinformatics 17: 455-460.
4. Corpett, F., Gouzy, J., and Kahn, D. 2000. ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 28: 267-269.
5. Dempster, A.P., Laid, N.M., and Rubin, D.B. 1977. Maximum likelihood from incomplete data via the EM algorithm (with discussion). J. Roy. Statist. Soc. Ser. B 39: 1-38.
6. Eisen, M.B., Spellman, P.T., Brown, P.O., and Bostein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci.95: 14863-14868.
7. Enright, A.J., Iliopoulos, I., Kyrpides, N.C., and Ouzounis, C.A. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90.
8. Ge, H., Liu, Z., Church, G.M., and Vidal, M. 2001. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet. 29: 482-486.
9. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., et al. 1996. Life with 6000 genes. Science 274: 546-567.
10. Gomez, G.M., Lo, S.H., and Rzhetsky, A. 2001. Probabilistic prediction of unknown metabolic and signal-transduction networks. Genetics 159: 1291-1298.
11. Grigoriev, A. 2001. A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acid Res. 29: 3513-3519.
12. Hazbun, T.R. and Fields, S. 2001. Networking proteins in yeast. Proc. Natl. Acad. Sci. 98: 4277-4278.
13. Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S., Sakaki, Y. 2000. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. 97: 1143-1147.
14. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. 2001a. A Comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. 98: 4569-4574.
15. Ito, T., Chiba, T., and Yoshida, M. 2001b. Exploring the protein interactome using comprehensive two hybrid projects. Trends Biotechnol. 19: S23-S27.
16. Legrain, P. and Selig, L. 2000. Genome-wide protein interaction maps using two-hybrid systems. FEBS Lett. 480: 32-36.
17. Lockhart, D.J. and Winzeler, E.A. 2000. Genomics, gene expression and DNA arrays. Nature 405: 827-836.
18. Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O., and Eisenberg, D. 1999a. Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753.
19. Marcotte, E.M., Pellegrini, M., Thompson, M.J., Yeates, T.O., and Eisenberg, D. 1999b. A combined algorithm for genome-wide prediction of protein function. Nature 402: 83-86.
20. Mewes, H.W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S., and Weil, B. 2002. MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 30: 31-34.
21. Mrowka, R., Patzak, A., and Herzel, H. 2001. Is there a bias in proteome research? Genome Res. 11: 1971-1973.
22. Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D., and Yeates, T.O. 1999. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl. Acad. Sci. 96: 4285-4288.
23. Rain, J.C., Selig, L., Reuse, H.D., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J., Schachter, V., et al. 2001. The protein-protein interaction map of Helicobacter pylori. Nature 409: 211-215.
24. Sprinzak, E. and Margalit, H. 2001. Correlated sequence-signatures as markers of protein-protein interaction. J. Mol. Biol. 311: 681-692.
25. 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. 2000. A Comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
26. Wojcik, J. and Schachter, V. 2001. Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics 17: S296-S305.