Protein function the post-genomic era

Nature

Volumn 405, Issue 6788, 2000, Pages 823-826

  Eisenberg, David ^a   Marcotte, Edward M ^a   Xenarios, Ioannis ^a   Yeates, Todd O ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

GENE EXPRESSION; GENE FUNCTION; GENE SEQUENCE; GENETIC LINKAGE; GENOME; HUMAN; INFORMATION PROCESSING; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; REVIEW; VALIDATION PROCESS;

ANIMALS; BIOTECHNOLOGY; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; GENOME; PHYLOGENY; PROTEINS;

EID: 0034660322     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/35015694     Document Type: Review

References (26)

1. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
2. The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018 (1998).
3. Chervitz, S. A. et al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282, 2022-2028 (1998).
4. Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33-36 (2000).
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. Natl Acad. Sci. USA 97, 1143-1147 (2000).
7. Alizadeh, A. A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503-511 (2000).
8. Lashkari, D. A. et al. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl Acad. Sci. USA 94, 13057-13062 (1997).
9. Brown, P. O. & Botstein, D. Exploring the new world of the genome with DNA microarrays. Nature Genet. 21, 33-37 (1999).
10. Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863-14868 (1998).
11. Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O. & Eisenberg, D. A combined algorithm for genome-wide prediction of protein function. Nature 402, 83-86 (1999).
12. Marcotte, E. M. et al. Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753 (1999).
13. Dandekar, T., Snel, B., Huynen, M. & Bork, P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 25, 324-328 (1998).
14. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D. & Maltsev, N. The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA 96, 2896-2901 (1999).
15. Enright, A. J., Iliopoulos, I., Kyrpides, N. C. & Ouzounis, C. A. Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 86-90 (1999).
16. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad Sci. USA 96, 4285-4288 (1999).
17. Andrade, M. A. & Valencia, A. Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. Bioinformatics 14, 600-607 (1998).
18. Kim, S. H. Structural genomics of microbes: an objective. Curr. Opin. Struct. Biol. (in the press).
19. Xenarios, I. et al. DIP: the Database of Interacting Proteins. Nucleic Acids Res. 28, 289-291 (2000).
20. Wickner, R. H. [URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae. Science 264, 566-569 (1994).
21. Bork, P. et al. Predicting function: from genes to genomes and back. J. Mol. Biol. 283, 707-725 (1998).
22. Huynen, M., Dandekar, T. & Bork, P. Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett. 426, 1-5 (1998).
23. Hegyi, H. & Gerstein, M. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J. Mol. Biol. 288, 147-164 (1999).
24. Ouzounis, C. & Kyrpides, N. The emergence of major cellular processes in evolution. FEBS Lett. 390, 119-123 (1996).
25. Gaasterland, T. & Ragan, M. A. Constructing multigenome views of whole microbial genomes. Microb. Comp. Genomics 3, 177-192 (1998).
26. Wu, Q. & Maniatis, T. A striking organization of a large family of human neural cadherin-like cell adhesion genes. Cell 97, 779-790 (1999).