Yeast genomics: Past, present, and future promise

Functional and Integrative Genomics

Volumn 2, Issue 4-5, 2002, Pages 135-137

  Snyder, Michael ^a   Kumar, Anuj ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; GENOMIC DNA; MEMBRANE PROTEIN;

CHEMICAL ANALYSIS; EDITORIAL; FUNGAL GENETICS; GENE DISRUPTION; GENE EXPRESSION; GENOMICS; MASS SPECTROMETRY; MUTAGENESIS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; RNA ANALYSIS; SACCHAROMYCES CEREVISIAE; YEAST; GENETICS; GENOME;

SACCHAROMYCES CEREVISIAE;

GENOME, FUNGAL; GENOMICS; SACCHAROMYCES CEREVISIAE;

EID: 0036729053     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-002-0064-4     Document Type: Editorial

References (31)

1. Ball C, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM (2001) Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res 29:80-81
2. Burns N, Grimwade B, Ross-Macdonald PB, Choi E-Y, Finberg K, Roeder GS, Snyder M (1994) Large-scale characterization of gene expression, protein localization and gene disruption in Saccharomyces cerevisiae. Genes Dev 8:1087-1105
3. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2:65-73
4. Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Lennon-Hopkins K, Kondu P, Lengieza C, Lew-Smith JE, Tillberg M, Garrels JI (2001) YPD, PombePD and WormPD: model organism volumes of the BioKnowledge Library, an integrated resource for protein information. Nucleic Acids Res 29:75-79
5. DeRisi JE, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680-686
6. Futcher B, Latter GI, Monardo P, McLaughlin CS, Garrels JI (1999) A sampling of the yeast proteome. Mol Cell Biol 19:7357-7368
7. Gavin A-C, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon A-M, Cruciat C-M, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier M-A, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork R Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147
8. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with 6,000 genes. Science 274;546:563-567
9. Gygi SP, Rist B, Gerber SA, Tureck F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotech 17:994-999
10. Ho Y, Gruhler A, Heilbut A, Bader G, Moore L, Adams S-L, Millar A, Taylor P, Bennet K, Boutilier K, Yang L, Wolting C, Doaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Anderson JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183
11. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y (2000) 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
12. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533-538
13. Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, Cheung K-H, Miller P, Gerstein M, Roeder GS, Snyder M (2002a) Subcellular localization of the yeast proteome. Genes Dev 16:707-719
14. Kumar A, Cheung K-H, Tosches N, Masiar P, Liu Y, Miller P, Snyder M (2002b) The TRIPEES database: a community resource for yeast molecular biology. Nucleic Acids Res 30:73-75
15. Link AJ, Eng J, Schieltz DM, Carmack E, Mize GJ, Morris DR, Garvik BM, Yates JR III (1999) Direct analysis of protein complexes using mass spectrometry. Nat Biotechnol 17:676-682
16. MacBeath G, Schreiber SL (2000) Printing proteins as microarrays for high-throughput function determination. Science 289:1760-1763
17. Martzen MR, McCraith SM, Spinelli SL, Torres FM, Fields S, Grayhack EJ, Phizicky EM (1999) A Biochemical genomics approach for identifying genes by the activity of their products. Science 286:1153-1155
18. Mewes HW, Albermann K, Bahr M, Frishman D, Gleissner A, Hani J, Heumann K, Kleine K, Maieri A, Oliver SG, Pfeiffer F, Zollner A (1997) Overview of the yeast genome. Nature 387(suppl):7-8
19. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res 30:31-34
20. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SPA (1994) Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA 91:5022-5026
21. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306-2309
22. Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, Tyers M, Boone C, Friend SH (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287:873-878
23. Ross-MacDonald P, Coelho PSR, Roemer T, Agarwal S, Kumar A, Jansen R, Cheung K-H, Sheehan A, Symoniatis D, Umansky L, Heidtman M, Nelson FK, Iwasaki H, Hager K, Gerstein M, Miller P, Roeder GS, Snyder M (1999) Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402:413-418
24. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
25. Tong AHY, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CWV, Bussey H, Andrews B, Tyers M, Boone C (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294:2364-2368
26. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijyadamodar G, Yang M, Johnston M, Fields S, Rothberg JM (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627
27. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Hieter R Vogelstein B, Kinzler KW (1997) Characterization of the yeast transcriptome. Cell 88:243-251
28. Washburn MR Wolters D, Yates JR III (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19:242-247
29. 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 FS, Dow S, Bakkoury M-E, Foury F, Friend SH, Genialen E, Giaever G, Hegemann JH, Jones TW, 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, Storms RK, Veronneau S, Voet M, Volkaert G, Ward TR, Wysocki R, Yen GS, Yu K, Zimmerman K, Philippsen R Johnston M, Davis RW (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906
30. Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M (2000) Analysis of yeast protein kinases using protein chips. Nat Genet 26:283-289
31. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M (2001) Global analysis of protein activities using proteome chips. Science 293:2101-2105