Genomic analysis of essentiality within protein networks

Trends in Genetics

Volumn 20, Issue 6, 2004, Pages 227-231

  Yu, Haiyuan ^a   Greenbaum, Dov ^a   Lu, Hao Xin ^a   Zhu, Xiaowei ^a   Gerstein, Mark ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESSENTIAL AMINO ACID; PROTEIN DERIVATIVE; TRANSCRIPTION FACTOR;

CELL FRACTIONATION; CELL POPULATION; CORRELATION ANALYSIS; EXPERIMENTAL TEST; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE TARGETING; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; KNOCKOUT GENE; MOLECULAR INTERACTION; MOLECULAR MECHANICS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; REVIEW; STATISTICAL SIGNIFICANCE;

EID: 2442477788     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2004.04.008     Document Type: Short Survey

References (27)

1. Akerley B.J., et al. Systematic identification of essential genes by in vitro mariner mutagenesis. Proc. Natl. Acad. Sci. U. S. A. 95:1998;8927-8932
2. Ross-Macdonald P., et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature. 402:1999;413-418
3. Winzeler E.A., et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 285:1999;901-906
4. Thatcher J.W., et al. Marginal fitness contributions of nonessential genes in yeast. Proc. Natl. Acad. Sci. U. S. A. 95:1998;253-257
5. Steinmetz L.M., et al. Systematic screen for human disease genes in yeast. Nat. Genet. 31:2002;400-404
6. Deutschbauer A.M., et al. Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 99:2002;15530-15535
7. Zewail A., et al. Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin. Proc. Natl. Acad. Sci. U. S. A. 100:2003;3345-3350
8. Smith V., et al. Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science. 274:1996;2069-2074
9. Rieger K.J., et al. Chemotyping of yeast mutants using robotics. Yeast. 15:1999;973-986
10. Entian K.D., et al. Functional analysis of 150 deletion mutants in Saccharomyces cerevisiae by a systematic approach. Mol. Gen. Genet. 262:1999;683-702
11. True H.L., Lindquist S.L. A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature. 407:2000;477-483
12. Sakumoto N., et al. A series of double disruptants for protein phosphatase genes in Saccharomyces cerevisiae and their phenotypic analysis. Yeast. 19:2002;587-599
13. Albert R., et al. Diameter of the World-Wide Web. Nature. 401:1999;130-131
14. Albert R., Barabasi A.L. Statistical Mechanics of Complex Networks. Rev. Mod. Phys. 74:2002;47-97
15. Watts D.J., Strogatz S.H. Collective dynamics of 'small-world' networks. Nature. 393:1998;440-442
16. Yu H., et al. TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Res. 32:2004;328-337
17. Barabasi A.L., Albert R. Emergence of Scaling in Random Networks. Science. 286:1999;509-512
18. Albert R., et al. Error and attack tolerance of complex networks. Nature. 406:2000;378-382
19. Jeong H., et al. Lethality and centrality in protein networks. Nature. 411:2001;41-42
20. Fraser H.B., et al. Evolutionary rate in the protein interaction network. Science. 296:2002;750-752
21. Jansen R., et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 302:2003;449-453
22. Yu H., et al. Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet. 19:2003;422-427
23. Horak C.E., et al. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev. 16:2002;3017-3033
24. Guelzim N., et al. Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet. 31:2002;60-63
25. Lee T.I., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 298:2002;799-804
26. Wingender E., et al. The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 29:2001;281-283
27. Mewes H.W., et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 30:2002;31-34