Global protein function prediction from protein-protein interaction networks

Nature Biotechnology

Volumn 21, Issue 6, 2003, Pages 697-700

  Vazquez, Alexei ^a,b   Flammini, Alessandro ^b   Maritan, Amos ^b,c   Vespignani, Alessandro ^d  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b INFM   (Italy)

^c ABDUS SALAM INTERNATIONAL CENTRE FOR THEORETICAL PHYSICS   (Italy)

^d UNIVERSITÉ PARIS SUD   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; GENES; PROTEINS;

PROTEIN-PROTEIN INTERACTIONS;

BIOTECHNOLOGY;

PROTEOME;

ARTICLE; GENE DELETION; GENE EXPRESSION; GENE FUNCTION; GENE INSERTION; GENOMICS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; DATABASES, PROTEIN; FUNGAL PROTEINS; MACROMOLECULAR SUBSTANCES; PROTEIN BINDING; PROTEOMICS; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SENSITIVITY AND SPECIFICITY;

INSERTION SEQUENCES; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0038699587     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt825     Document Type: Article

References (16)

1. Hodgman, T.C. A historical perspective on gene/protein functional assignment. Bioinformatics 16, 10-15 (2000).
2. Zhang, M.Q. Promoter analysis of co-regulated genes in the yeast genome. Comput. Chem. 23, 233-250 (1999).
3. Harrington, H.C., Rosenow, C. & Retief, J. Monitoring gene expression using DNA microarrays. Curr. Opin. Microbiol. 3, 285-291 (2000).
4. Pellegrini, M., Marcotte, E., Thompson, M.J., Eisenberg, D. & Yeates, T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Nat. Acad. Sci. USA 96, 4285-4288 (1999).
5. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
6. Ito, T. et al. 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. Nat. Acad. Sci. USA 98, 4569-1147 (2001).
7. Schwikowski, B., Uetz, P. & Fields, S. A network of protein-protein interactions in yeast. Nat. Biotechnol. 18, 1257-1261 (2000).
8. Hishigaki, H., Nakai, K., Ono, T., Tanigami, A. & Tagaki, T. Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 18, 523-531 (2001).
9. Gavin, A. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).
10. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002).
11. Wagner, A. Robustness again mutations in genetic networks of yeast. Nat. Genet. 24, 355-361 (2000).
12. Jeong, H., Mason, S.P., Barabasi, A.L, & Oltwai, Z.W. Lethality and centrality in protein networks. Nature 411, 41 (2001).
13. Meyer, M.L. & Hieter, P. Protein networks - built by association. Nat. Biotechnol. 18, 1242-1243 (2000).
14. Wu, F.Y. The Potts Model. Rev. Mod. Phys. 54, 235-268 (1982).
15. The MIPS Comprehensive Yeast Genome Database (CYGD), http://mips.gsf.de/proj/yeast/CYGD/db/.
16. Kirkpatrick, S., Gelatt, C.D. & Vecchi, M.P. Optimization by simulated annealing. Science 220, 621-680 (1983).