Comparative interactomics

FEBS Letters

Volumn 579, Issue 8, 2005, Pages 1828-1833

  Cesareni, Gianni ^a   Ceol, Arnaud ^a   Gavrila, Caius ^a   Palazzi, Luisa Montecchi ^a   Persico, Maria ^a   Schneider, Maria Victoria ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

Author keywords

Evolution; High throughput experiment; Networks; Protein interaction

Indexed keywords

CAENORHABDITIS ELEGANS PROTEIN; DROSOPHILA PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; CAENORHABDITIS ELEGANS; CELL FUNCTION; CELL STIMULATION; COMPARATIVE GENE MAPPING; DROSOPHILA; GENE MUTATION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC ORGANIZATION; GENETIC VARIABILITY; GENOME; HIGH THROUGHPUT SCREENING; HUMAN; INFORMATION SYSTEM; LEARNING; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; NONHUMAN; OBSERVATION; OPEN READING FRAME; PRESSURE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; SHORT SURVEY; STRUCTURAL PROTEOMICS; VALIDATION PROCESS;

EID: 14844282107     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2005.01.064     Document Type: Short Survey

References (30)

1. M.A. Huynen, B. Snel, and V. van Noort Comparative genomics for reliable protein-function prediction from genomic data Trends Genet. 20 2004 340 344
2. A.C. Gavin Functional organization of the yeast proteome by systematic analysis of protein complexes Nature 415 2002 141 147
3. Y. Ho Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Nature 415 2002 180 183
4. T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc. Natl. Acad. Sci. USA 98 2001 4569 4574
5. P. Uetz A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 403 2000 623 627 (see comments)
6. S. Li A map of the interactome network of the metazoan C. elegans Science 303 2004 540 543
7. L. Giot A protein interaction map of Drosophila melanogaster Science 302 2003 1727 1736
8. M. Remm, C.E. Storm, and E.L. Sonnhammer Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J. Mol. Biol. 314 2001 1041 1052
9. L. Li, C.J. Stoeckert Jr., and D.S. Roos OrthoMCL: identification of ortholog groups for eukaryotic genomes Genome Res. 13 2003 2178 2189
10. S.B. Cannon, and N.D. Young OrthoParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies BMC Bioinform. 4 2003 35
11. M. Pellegrini, E.M. Marcotte, M.J. Thompson, D. Eisenberg, and T.O. Yeates Assigning protein functions by comparative genome analysis: protein phylogenetic profiles Proc. Natl. Acad. Sci. USA 96 1999 4285 4288
12. E.M. Marcotte, M. Pellegrini, H.L. Ng, D.W. Rice, T.O. Yeates, and D. Eisenberg Detecting protein function and protein-protein interactions from genome sequences Science 285 1999 751 753
13. A.J. Enright, I. Iliopoulos, N.C. Kyrpides, and C.A. Ouzounis Protein interaction maps for complete genomes based on gene fusion events Nature 402 1999 86 90
14. F. Pazos, and A. Valencia In silico two-hybrid system for the selection of physically interacting protein pairs Proteins 47 2002 219 227
15. U. Gobel, C. Sander, R. Schneider, and A Correlated mutations and residue contacts in proteins Proteins 18 1994 309 317
16. Hulo, N. et al. (2004) Recent improvements to the PROSITE database Nucleic Acids Res 32 Database issue, D134-7
17. C. Landgraf, S. Panni, L. Montecchi-Palazzi, L. Castagnoli, J. Schneider-Mergener, R. Volkmer-Engert, and G. Cesareni Protein interaction networks by proteome peptide scanning PLoS Biol. 2 2004 E14
18. A.J. Walhout, R. Sordella, X. Lu, J.L. Hartley, G.F. Temple, M.A. Brasch, N. Thierry-Mieg, and M Protein interaction mapping in C. elegans using proteins involved in vulval development Science 287 2000 116 122
19. L.R. Matthews, P. Vaglio, J. Reboul, H. Ge, B.P. Davis, J. Garrels, S. Vincent, and M. Vidal Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs" Genome Res. 11 2001 2120 2126
20. C. von Mering, R. Krause, B. Snel, M. Cornell, S.G. Oliver, S. Fields, and P. Bork Comparative assessment of large-scale data sets of protein-protein interactions Nature 417 2002 399 403
21. B. Lehner, and A.G. Fraser A first-draft human protein-interaction map Genome Biol. 5 2004 R63
22. A. Zanzoni, L. Montecchi-Palazzi, M. Quondam, G. Ausiello, M. Helmer-Citterich, and G. Cesareni MINT: a Molecular INTeraction database FEBS Lett. 513 2002 135 140
23. G.D. Bader, D. Betel, and C.W. Hogue BIND: the biomolecular interaction network database Nucleic Acids Res. 31 2003 248 250
24. H. Hermjakob IntAct: an open source molecular interaction database Nucleic Acids Res. 32 Database issue 2004 D452 D455
25. I. Xenarios, L. Salwinski, X.J. Duan, P. Higney, S.M. Kim, and D. Eisenberg DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions Nucleic Acids Res. 30 2002 303 305
26. H. Hermjakob The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data Nat. Biotechnol. 22 2004 177 183
27. S. Peri Development of human protein reference database as an initial platform for approaching systems biology in humans Genome Res. 13 2003 2363 2371
28. H. Yu Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs Genome Res. 14 2004 1107 1118
29. M. Koyuturk, A. Grama, and W. Szpankowski An efficient algorithm for detecting frequent subgraphs in biological networks Bioinformatics 20 Suppl 1 2004 I200 I207
30. B.P. Kelley, R. Sharan, R.M. Karp, T. Sittler, D.E. Root, B.R. Stockwell, and T. Ideker Conserved pathways within bacteria and yeast as revealed by global protein network alignment Proc. Natl. Acad. Sci. USA 100 2003 11394 11399