Global analysis of gene function in yeast by quantitative phenotypic profiling

Molecular Systems Biology

Volumn 2, Issue , 2006, Pages

  Brown, James A ^a   Sherlock, Gavin ^a   Myers, Chad L ^b   Burrows, Nicola M ^a   Deng, Changchun ^a   Wu, H Irene ^a   McCann, Kelly E ^a   Troyanskaya, Olga G ^b   Brown, J Martin ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Princeton University   (United States)

Author keywords

Deletion pool; Functional genomics; Hierarchical clustering; Phenotypic profiling; Yeast

Indexed keywords

CYTOSTATIC AGENT; CYTOTOXIC AGENT; FUNGAL DNA;

ARTICLE; CONTROLLED STUDY; DNA DAMAGE; DNA REPAIR; GENE CLUSTER; GENE DELETION; GENE FUNCTION; GENOME; HOMOZYGOTE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SACCHAROMYCES CEREVISIAE;

CLUSTER ANALYSIS; DNA DAMAGE; DNA REPAIR; GENE DELETION; GENES, FUNGAL; METHODS; PHENOTYPE; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCETALES;

EID: 33745454509     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb4100043     Document Type: Article

References (27)

1. Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, Buzadzija K, Cavero R, D'Abreo C, Donaldson I, Dorairajoo D, Dumontier MJ, Dumontier MR, Earles V, Farrall R, Feldman H, Garderman E, Gong Y, Gonzaga R, Grytsan V, Gryz E, Gu V, Haldorsen E, Halupa A, Haw R, Hrvojic A, Hurrell L, Isserlin R, Jack F, Juma F, Khan A, Kon T, Konopinsky S, Le V, Lee E, Ling S, Magidin M, Moniakis J, Montojo J, Moore S, Muskat B, Ng I, Paraiso JP, Parker B, Pintilie G, Pirone R, Salama JJ, Sgro S, Shan T, Shu Y, Siew J, Skinner D, Snyder K, Stasiuk R, Strumpf D, Tuekam B, Tao S, Wang Z, White M, Willis R, Wolting C, Wong S, Wrong A, Xin C, Yao R, Yates B, Zhang S, Zheng K, Pawson T, Ouellette BF, Hogue CW (2005) The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res 33: D418-D424
2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29
3. Ball CA, Awad IA, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G (2005) The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res 33: D580-D582
4. Birrell GW, Giaever G, Chu AM, Davis RW, Brown JM (2001) A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity. Proc Natl Acad Sci USA 98: 12608-12613
5. Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G (2004) GO:TermFinder - open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 20: 3710-3715
6. Brachat S, Dietrich FS, Voegeli S, Zhang Z, Stuart L, Lerch A, Gates K, Gaffney T, Philippsen P (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biol 4: R45
7. Breitkreutz BJ, Stark C, Tyers M (2003) The GRID: the general repository for interaction datasets. Genome Biol 4: R23
8. Cadet J, Sage E, Douki T (2005) Ultraviolet radiation-mediated damage to cellular DNA. Mutat Res 571: 3-17
9. Game JC, Birrell GW, Brown JA, Shibata T, Baccari C, Chu AM, Williamson MS, Brown JM (2003) Use of a genome-wide approach to identify new genes that control resistance of Saccharomyces cerevisiae to ionizing radiation. Radiat Res 160: 14-24
10. Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO (2001) Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell 12: 2987-3003
11. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257
12. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391
13. Guthrie C, Fink GR (eds) (1991) Guide to Yeast Genetics and Molecular Biology. San Diego: Academic Press Inc
14. Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B (2004) Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol 5: R95 (Epub Nov 29)
15. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126
16. Lee I, Date SV, Adai AT, Marcotte EM (2004) A probabilistic functional network of yeast genes. Science 306: 1555-1558
17. Lee W, St Onge RP, Proctor M, Flaherty P, Jordan MI, Arkin AP, Davis RW, Nislow C, Giaever G, Snyder M (2005) Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet 1: e24
18. Peters KB, Brown JM (2002) Tirapazamine: a hypoxia-activated topoisomerase II poison. Cancer Res 62: 5248-5253
19. Scherens B, Goffeau A (2004) The uses of genome-wide yeast mutant collections. Genome Biol 5: 229.221-229.228.
20. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C (2004) Global mapping of the yeast genetic interaction network. Science 303: 808-813
21. Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci USA 100: 8348-8353
22. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403
23. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Prèuss M, Reuter I, Schacherer F (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28: 316-319
24. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M'Rabet N, Menard P, Mittmann M, Pai C, Rebischung C, Revuelta JL, Riles L, Roberts CJ, Ross-MacDonald P, Scherens B, Snyder M, Sookhai-Mahadeo S, Stroms RK, Veronneau S, Voet M, Volckaert G, Ward TR, Wysocki R, Yen GS, Yu K, Zimmermann K, Philippsen P, Johnston M, Davis RW (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906
25. Wu HI, Brown JA, Dorie MJ, Lazzeroni L, Brown JM (2004) Genome-wide identification of genes conferring resistance to the anticancer agents cisplatin, oxaliplatin, and mitomycin C. Cancer Res 64: 3940-3948
26. Zhou BB, Elledge SJ (2000) The DNA damage response: putting checkpoints in perspective. Nature 408: 433-439
27. Zhu J, Zhang MQ (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15: 607-611