Systematic interpretation of genetic interactions using protein networks

Nature Biotechnology

Volumn 23, Issue 5, 2005, Pages 561-566

  Kelley, Ryan ^a,b   Ideker, Trey ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MUTAGENESIS; PROTEINS; YEAST;

GENETIC INTERACTIONS; MUTATION;

GENES;

ALGORITHM; GENE DELETION; GENE INTERACTION; GENE MUTATION; GENETIC ANALYSIS; GENETIC MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; REVIEW; SACCHAROMYCES CEREVISIAE; YEAST; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; PHYSIOLOGY; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION;

SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHMS; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; MODELS, GENETIC; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION;

EID: 22844450110     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1096     Document Type: Review

References (37)

1. Guarente, L. Synthetic enhancement in gene interaction: a genetic tool come of age. Trends Genet. 9, 362-366 (1993).
2. Avery, L. & Wasserman, S. Ordering gene function: the interpretation of epistasis in regulatory hierarchies. Trends Genet. 8, 312-316 (1992).
3. Thomas, J.H. Thinking about genetic redundancy. Trends Genet. 9, 395-399 (1993).
4. Hartman, J.L., Garvik, B. & Hartwell, L. Principles for the buffering of genetic variation. Science 291, 1001-1004 (2001).
5. Sham, P. Shifting paradigms in gene-mapping methodology for complex traits. Pharmacogenomics 2, 195-202 (2001).
6. Dolma, S., Lessnick, S.L., Hahn, W.C. & Stockwell, B.R. Identification of genotype-selective antitumor agents using synthetic lethal chemical screening in engineered human tumor cells. Cancer Cell 3, 285-296 (2003).
7. Forsburg, S.L. The art and design of genetic screens: yeast. Nat. Rev. Genet. 2, 659-668 (2001).
8. Tong, A.H. et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364-2368 (2001).
9. Ooi, S.L., Shoemaker, D.D. & Boeke, J.D. DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nat. Genet. 35, 277-286 (2003).
10. Tong, A.H. et al. Global mapping of the yeast genetic interaction network. Science 303, 808-813 (2004).
11. Li, S. et al. A map of the interactome network of the metazoan C. elegans. Science 303, 540-543 (2004).
12. Rain, J.C. et al. The protein-protein interaction map of Helicobacter pylori. Nature 409, 211-215 (2001).
13. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
14. Giot, L. et al. A protein interaction map of Drosophila melanogaster. Science 302, 1727-1736 (2003).
15. 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).
16. Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002).
17. Gavin, A-C., Bösche, M., Krause, R., Grandi, P. & Marzioch, M. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).
18. Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
19. Harbison, C.T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).
20. Ozier, O., Amin, N. & Ideker, T. Global architecture of genetic interactions on the protein network. Nat. Biotechnol. 21, 490-491 (2003).
21. Tucker, C.L. & Fields, S. Lethal combinations. Nat. Genet. 35, 204-205 (2003).
22. Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
23. Mewes, H.W. et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 30, 31-34 (2002).
24. Xenarios, I. et al. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30, 303-305 (2002).
25. Kanehisa, M., Goto, S., Kawashima, S. & Nakaya, A. The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002).
26. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).
27. Gene Ontology Consortium. Creating the gene ontology resource: design and implementation. Genome Res. 11, 1425-1433 (2001).
28. Zar, J.H. Biostatistical Analysis, edn. 3 (Prentice Hall, New Jersey, 1996).
29. Kendall, S.M., Stuart, A. & Ord, J.K. Kendall's Advanced Theory of Statistics, edn. 5 (Oxford University Press, NY, 1987).
30. Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824-827 (2002).
31. Geissler, S., Siegers, K. & Schiebel, E. A novel protein complex promoting formation of functional alpha- and gamma-tubulin. EMBO J. 17, 952-966 (1998).
32. Kahana, J.A. et al. The yeast dynactin complex is involved in partitioning the mitotic spindle between mother and daughter cells during anaphase B. Mol. Biol. Cell 9, 1741-1756 (1998).
33. Pidoux, A.L. & Allshire, R.C. Centromeres: getting a grip of chromosomes. Curr. Opin. Cell Biol. 12, 308-319 (2000).
34. Pfeffer, S.R. Membrane transport: retromer to the rescue. Curr. Biol. 11, R109-R111 (2001).
35. Siniossoglou, S., Peak-Chew, S.Y. & Pelham, H.R. Ric1p and Rgp1p form a complex that catalyses nucleotide exchange on Ypt6p. EMBO J. 19, 4885-4894 (2000).
36. Hwang, W.W. et al. A conserved RING finger protein required for histone H2B monoubiquitination and cell size control. Mol. Cell 11, 261-266 (2003).
37. Sharan, R., Ideker, T., Kelley, B.P., Shamir, R. & Karp, R.M. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology-RECOMB, 282-289 (ACM Press, New York, 2004)