Protein-protein interaction map inference using interacting domain profile pairs

Bioinformatics

Volumn 17, Issue SUPPL. 1, 2001, Pages

  Wojcik, Jérôme ^a   Schächter, Vincent ^a  

^a Hybrigenics SA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; GENETICS; MACROMOLECULE; METABOLISM; MOLECULAR GENETICS; PEPTIDE MAPPING; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; STATISTICS;

ALGORITHMS; AMINO ACID SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ESCHERICHIA COLI PROTEINS; MACROMOLECULAR SUBSTANCES; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PEPTIDE MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE; SOFTWARE DESIGN;

EID: 0035224503     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.suppl_1.S296     Document Type: Article

References (25)

1. Bansal, A.K. (1999). An automated comparative analysis of 17 complete microbial genomes. Bioinformatics, 15, 900-8.
2. Bork, P., Dandekar, T., Diaz-Lazcoz, Y., Eisenhaber, F., Huynen, M. and Yuan, Y. (1998). Predicting function: from genes to genomes and back. J Mol Biol., 283, 707-25.
3. Dandekar, T., Snel, B., Huynen, M. and Bork, P. (1998). Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci., 23, 324-8.
4. 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, 14863-8.
5. Eisenberg, D., Marcotte, E.M., Xenarios, I. and Yeates, T.O. (2000). Protein function in the post-genomic era. Nature, 405, 823-6.
6. 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.
7. Fellenberg, M., Albermann, K., Zollner, A., Mewes, H.W. and Hani, J. (2000). Integrative analysis of protein interaction data. ISMB, 8, 152-61.
8. Flajolet, M., Rotondo, G., Daviet, L., Bergametti, F., Inchausp, G., Tiollais, P., Transy, C. and Legrain, P. (2000). A genomic approach of the hepatitis C virus generates a protein interaction map. Gene, 242, 369-379.
9. Fromont-Racine, M., Mayes, A.E., Brunet-Simon, A., Rain, J.C., Colley, A., Dix, I., Decourty, L., Joly, N., Ricard, F., Beggs, J.D. and Legrain, P. (2000). Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast, 17, 95-110.
10. Fromont-Racine, M., Rain, J.C. and Legrain, P. (1997). Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat Genetics, 16, 277-82.
11. Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S. and 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 USA, 97, 1143-7.
12. Karp, P.D., Ouzounis, C. and Paley, S. (1996). HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae. ISMB, 4, 116-24.
13. Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O. and Eisenberg, D. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science, 285, 751-3.
14. Marcotte, E.M., Pellegrini, M., Thompson, M.J., Yeates, T.O. and Eisenberg, D. (1999). A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83-6.
15. McCraith, S., Holtzman, T., Moss, B. and Fields, S. (2000). Genome-wide analysis of vaccinia virus protein- protein interactions. Proc Natl Acad Sci USA, 97, 4879-84.
16. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D. and Maltsev, N. (1999). The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA, 96, 2896-901.
17. Pearson, W.R. (2000). Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol, 132, 185-219.
18. 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 USA, 96, 4285-8.
19. Rain, J.C., Selig, L., de Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J., Schächter, V., Chemama, Y., Labigne, A. and Legrain, P. (2001). The protein-protein interaction map of Helicobacter pylori. Nature, 409, 211-216.
20. Schwikowski, B., Uetz, P. and Fields, S. (2000). A network of protein-protein interactions in yeast. Nat Biotechnol, 18, 1257-61.
21. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 22, 4673-80.
22. Tomb, J.F., et al. (1997). The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature, 388, 539-47.
23. Uetz, P., et al. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-27.
24. Walhout, A.J., Sordella, R., Lu, X., Hartley, J.L., Temple, G.F., Brasch, M.A., Thierry-Mieg, N. and Vidal, M. (2000). Protein interaction mapping in C. elegans using proteins involved in vulval development. Science, 287, 116-22.
25. Walhout, A.J.M. and Vidal, M. (2001). Protein interaction maps for model organisms. Nat Rev, Mol Cell Biol., 2, 55-62.