Evolution and topology in the yeast protein interaction network

Genome Research

Volumn 14, Issue 7, 2004, Pages 1310-1314

  Wuchty, Stefan ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN;

ARTICLE; DATA ANALYSIS; GENETIC CONSERVATION; GENETIC CORRELATION; GENETIC DISTANCE; MOLECULAR EVOLUTION; ORTHOLOGY; PRIORITY JOURNAL; PROBABILITY; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; TWO HYBRID SYSTEM;

ANIMALS; ARABIDOPSIS PROTEINS; CAENORHABDITIS ELEGANS PROTEINS; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; HUMANS; MICE; PROTEIN INTERACTION MAPPING; PROTEINS; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 3543099834     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2300204     Document Type: Article

References (27)

1. Albert, R., Jeong, H., and Barabási, A.-L. 2000. Error and attack tolerance of complex networks. Nature 406: 378-382.
2. Costanzo, M., Crawford, M., Hirschman, J.E., Kranz, J.E., Olsen, P., Robertson, L.S., Skrzypek, M.S., Braun, B.R., Hopkins, K.L., Kondu, P., et al. 2001. YPD, PombePD and WormPD: Model organism volumes of the BioKnowledge Library, an integrated resource for protein information. Nucl. Acids Res. 29: 75-79.
3. Fraser, H., Hirsh, A., Steinmetz, L., Scharfe, C., and Feldman, M. 2002. Evolutionary rate in the protein interaction network. Science 296: 750-752.
4. Fraser, H., Wall, D., and Hirsh, A. 2003. A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol. Biol. 3: 11.
5. Gavin, A., Boesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
6. Goldberg, D. and Roth, F. 2003. Assessing experimentally derived interactions in a small-world. Proc. Natl. Acad. Sci. 100: 4372-4376.
7. Goldstein, M., Morris, S., and Yen, G. 2004. Fitting to the power-law distribution. http://arxiv.org/abs/cond-mat/0402322.
8. Grishin, N. 1997. Estimation of evolutionary distances from protein spatial structures. J. Mol. Evol. 45: 359-369.
9. Hahn, M., Conant, G., and Wagner, A. 2002. Molecular evolution in large genetic networks: Connectivity does not equal importance. SFI working paper, 02-08-039.
10. Hazbun, T. and Fields, S. 2001. Networking proteins in yeast. Proc. Natl. Acad. Sci. 98: 4277-4278.
11. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
12. Hurst, L. and Smith, N. 1999. Do essential genes evolve slowly? Curr. Biol. 9: 747-750.
13. Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S., and Sakaki, Y. 2000. Towards 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. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. 98: 4569-4574.
15. Jeong, H., Mason, S., Barabási, A.-L., and Oltvai, Z. 2001. Lethality and centrality in protein networks. Nature 411: 41-42.
16. Jordan, I., Rogozin, I., Wolf, Y., and Koonin, E. 2002. Essential genes are evolutionary more conserved than are nonessential genes in bacteria. Genome Res. 12: 962-968.
17. Jordan, I., Wolf, Y., and Koonin, E. 2003a. Correction: No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly. BMC Evol. Biol. 3.
18. Jordan, I., Wolf, Y., and Koonin, E. 2003b. No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly. BMC Evol. Biol. 3.
19. Koski, L. and Golding, G. 2001. The closest blast hit is often not the nearest neighbor. J. Mol. Evol. 52: 540-542.
20. Park, J., Lappe, M., and Teichmann, A. 2001. Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J. Mol. Biol. 307: 929-938.
21. Remm, M., Storm, C., and Sonnhammer, E. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314: 1041-1052.
22. 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 of Saccharomyces cerevisiae. Nature 403: 623-627.
23. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S., Fields, S., and Bork, P. 2003. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
24. Wagner, A. 2001. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18: 1283-1292.
25. Wall, D., Fraser, H., and Hirsh, A. 2003. Detecting putative orthologs. Bioinformatics 19: 1710-1711.
26. Wuchty, S. 2002. Interaction and domain networks of yeast. Proteomics 2: 1715-1723.
27. Xenarios I., Salwinski, L., Duan, X., Higney, P., Kim, S.-M., and Eisenberg, D. 2002. Dip, the database of interacting proteins: A research tool for studying cellular networks of protein interactions. Nucl. Acids Res. 30: 303-305.