Systematic identification of gene annotation errors in the widely used yeast mutation collections

Nature Methods

Volumn 9, Issue 4, 2012, Pages 373-378

  Ben Shitrit, Taly ^a   Yosef, Nir ^b,c   Shemesh, Keren ^a   Sharan, Roded ^a   Ruppin, Eytan ^a   Kupiec, Martin ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b HARVARD UNIVERSITY   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RAPAMYCIN;

ALGORITHM; ARTICLE; CONTROLLED STUDY; DRUG RESPONSE; GENE ANNOTATION ERROR; GENE IDENTIFICATION; GENE MUTATION; GENETIC ANALYSIS; GENETIC SCREENING; MOLECULAR GENETICS; NEIGHBORING GENE EFFECT; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE REGULATORY NETWORKS; MOLECULAR SEQUENCE ANNOTATION; MUTATION; PHENOTYPE; RESEARCH DESIGN; SACCHAROMYCES CEREVISIAE; SOFTWARE;

EID: 84859189663     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.1890     Document Type: Article

References (38)

1. Hillenmeyer, M.E. et al. The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320, 362-365 (2008).
2. Hughes, T.R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109-126 (2000).
3. Costanzo, M. et al. The genetic landscape of a cell. Science 327, 425-431 (2010).
4. Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
5. Tong, A.H. et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364-2368 (2001).
6. Pan, X. et al. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124, 1069-1081 (2006).
7. Addinall, S.G. et al. A genomewide suppressor and enhancer analysis of cdc13-1 reveals varied cellular processes influencing telomere capping in Saccharomyces cerevisiae. Genetics 180, 2251-2266 (2008).
8. Tian, W. et al. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol. 9 (suppl. 1), S7 (2008).
9. Kelley, R. & Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nat. Biotechnol. 23, 561-566 (2005).
10. van Wageningen, S. et al. Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell 143, 991-1004 (2010).
11. Breslow, D.K. et al. A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat. Methods 5, 711-718 (2008).
12. Ben-Aroya, S. et al. Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae. Mol. Cell 30, 248-258 (2008).
13. Li, Z. et al. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat. Biotechnol. 29, 361-367 (2011).
14. Shachar, R., Ungar, L., Kupiec, M., Ruppin, E. & Sharan, R. A systems-level approach to mapping the telomere length maintenance gene circuitry. Mol. Syst. Biol. 4, 172 (2008).
15. Ungar, L. et al. A genome-wide screen for essential yeast genes that affect telomere length maintenance. Nucleic Acids Res. 37, 3840-3849 (2009).
16. Yosef, N. et al. Toward accurate reconstruction of functional protein networks. Mol. Syst. Biol. 5, 248 (2009).
17. Dittrich, M., Klau, G., Rosenwald, A., Dandekar, T. & Müller, T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 24, i223-i231 (2008).
18. Huang, S.S. & Fraenkel, E. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci. Signal. 2, ra40 (2009).
19. Yosef, N. et al. ANAT-a software tool for reconstructing and analyzing functional networks of proteins. Sci. Signal. 4, l1 (2011).
20. Askree, S.H. et al. A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length. Proc. Natl. Acad. Sci. USA 101, 8658-8663 (2004).
21. Gatbonton, T. et al. Telomere length as a quantitative trait: genome-wide survey and genetic mapping of telomere length-control genes in yeast. PLoS Genet. 2, e35 (2006).
22. Parsons, A.B. et al. Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways. Nat. Biotechnol. 22, 62-69 (2004).
23. Chan, T.F., Carvalho, J., Riles, L. & Zheng, X.F. A chemical genomics approach toward understanding the global functions of the target of rapamycin protein (TOR). Proc. Natl. Acad. Sci. USA 97, 13227-13232 (2000).
24. Crespo, J.L. & Hall, M.N. Elucidating TOR signaling and rapamycin action: lessons from Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 66, 579-591 (2002).
25. Reid, R.J. et al. Selective ploidy ablation, a high-throughput plasmid transfer protocol, identifies new genes affecting topoisomerase I-induced DNA damage. Genome Res. 21, 477-486 (2011).
26. Gustavsson, M. & Ronne, H. Evidence that tRNA modifying enzymes are important in vivo targets for 5-fluorouracil in yeast. RNA 14, 666-674 (2008).
27. Tuller, T. et al. Higher-order genomic organization of cellular functions in yeast. J. Comput. Biol. 16, 303-316 (2009).
28. Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033-1037 (2009).
29. Snyder, M. & Gallagher, J.E. Systems biology from a yeast omics perspective. FEBS Lett. 583, 3895-3899 (2009).
30. Sharan, R. et al. Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. USA 102, 1974-1979 (2005).
31. Gavin, A.C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).
32. Krogan, N.J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643 (2006).
33. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569-4574 (2001).
34. Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
35. Reguly, T. et al. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J. Biol. 5, 11 (2006).
36. Breitkreutz, B.J. et al. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res. 36 Database issue, D637-D640 (2008).
37. Yosef, N. et al. ANAT: a tool for constructing and analyzing functional protein networks. Sci. Signal. 4, pl1 (2011).
38. Charikar, M. et al. Approximation algorithms for directed Steiner problems. J. Algorithms 33, 73-91 (1999).