Yeast as a touchstone in post-genomic research: Strategies for integrative analysis in functional genomics

Journal of Biochemistry and Molecular Biology

Volumn 37, Issue 1, 2004, Pages 93-106

  Castrillo, Juan I ^a   Oliver, Stephen G ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Functional genomics; Integrative studies; Saccharomyces cerevisiae; Schizosaccharomyces pombe; Systems biology

Indexed keywords

BIOINFORMATICS; BOTTLENECK POPULATION; DNA MICROARRAY; GENE IDENTIFICATION; GENOME ANALYSIS; GENOMICS; INFORMATION PROCESSING; PHENOTYPE; REGULATORY MECHANISM; REVIEW; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SYSTEM ANALYSIS; YEAST;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE;

EID: 1642486494     PISSN: 12258687     EISSN: None     Source Type: Journal    
DOI: 10.5483/bmbrep.2004.37.1.093     Document Type: Review

References (196)

1. Adams, A. (2003) Metabolomics: Small-molecule omics. The Scientist 17, 38-40.
2. Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F. et al. (2000) The genome sequence of Drosophila melanogaster. Science 287, 2185-2195.
3. Ahmad, F., Kaplan, C. D. and Stewart, E. (2002). Helicase activity is only partially required for Schizosaccharomyces pombe Rqhlp function. Yeast 19, 1381-1398.
4. Allen, J., Davey, H. M., Broadhurst, D., Heald, J. K., Rowland, J. J., Oliver, S. G. and Kell, D. B. (2003) High-throughput classification of yeast mutants using metabolic footprinting. Nat. Biotechnol. 21, 692-696.
5. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
6. Bach, S., Talarek, N., Andrieu, T., Vierfond, J. M., Mettey, Y., Galons, H., Dormont, D., Meijer, L., Cullin, C. and Blondel, M. (2003) Isolation of drugs active against mammalian prions using a yeast-based screening assay. Nat. Biotechnol. 21, 1075-1081.
7. Bader, G. D., Betel, D. and Hogue, C. W. V. (2003) BIND: the biomolecular interaction network database. Nucleic Acids Res. 31, 248-250.
8. Baganz, F., Hayes, A., Marren, D., Gardner, D. C. J. and Oliver, S. G. (1997) Suitability of replacement markers for functional analysis studies in Saccharomyces cerevisiae. Yeast 13, 1563-1573.
9. Baganz, F., Hayes, A., Farquhar, R., Butler, P. R., Gardner, D. C. J. and Oliver, S. G. (1998) Quantitative analysis of yeast gene function using competition experiments in continuous culture. Yeast 14, 1417-1427.
10. Bahls, C., Weitzma, J. and Gallaguer, R. (2003). Model organisms. The Scientist 17, Suppl. 1.
11. Blaxter, M. (2003) Comparative genomics: Two worms are better than one. Nature 426, 395-396.
12. Boer, V. M., de Winde, J. H., Pronk, J. T. and Piper, M. D. W. (2003). The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J. Biol. Chem. 278, 3265-3274.
13. Bono, H., Yagi, K., Kasukawa, T., Nikaido, I., Tominaga, N., Miki, R., Mizuno, Y., Tomaru, Y., Goto, H., Nitanda, H. et al. (2003) Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res. 13, 1318-1323.
14. Boube, M., Joulia, L., Cribbs, D. L., Bourbon, H. M. (2002) Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 110, 143-151.
15. Brancia, F. L., Butt, A., Beynon, R. J., Hubbard, S. J., Gaskell, S. J. and Oliver, S. G. (2001) A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics. Electrophoresis 22, 552-559.
16. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics 29, 365-371.
17. Brown, A. J. P., Planta, R. J., Restuhadi, F., Bailey, D. A., Butler, P. R., Cadahia, J. L., Cerdan, M. E., De Jonge, M., Gardner, D. C. J., Gent, M. E. et al. (2001) Transcript analysis of 1003 novel yeast genes using high-throughput northern hybridisations. EMBO J. 20, 3177-3186.
18. Bryant, C. H., Muggleton, S. H., Oliver, S. G., Kell, D. B., Reiser, P. and King, R. D. (2001) Combining active inductive programming, active learning and robotics to discover the function of genes. Electron. Trans. Artif. Intell. 5, 1-36.
19. Castrillo, J. I. and Ugalde, U. O. (1994) A general model of yeast energy metabolism in aerobic chemostat culture. Yeast 10, 185-197.
20. Castrillo, J. I., Hayes, A., Mohammed, S., Gaskell, S. J. and Oliver, S. G. (2003) An optimised protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry 62, 929-937.
21. th Biochemical Science Report Howard Hughes Medical Institute. On-line publication (http://www.hhmi. org).
22. Chang, F. and Peter, M. (2003) Yeasts make their mark. Nature Cell Biol. 5, 294-299.
23. Chatterjee, M. T., Khalawan, S. A. and Curran, B. P. (2001). Subtle alterations in growth medium composition can dramatically alter the percentage of unsaturated fatty acids in the yeast Saccharomyces cerevisiae. Yeast 18, 81-88.
24. Chen, C. N., Porubleva, L., Shearer, G., Svrakic, M., Holden, L. G., Dover, J. L., Johnston, M., Chitnis, P. R. and Kohl, D. H. (2003) Associating protein activities with their genes: rapid identification of a gene encoding a methylglyoxal reductase in the yeast Saccharomyces cerevisiae. Yeast 20, 545-554.
25. Chervitz, S. A., Aravind, L., Sherlock, G., Ball, C. A., Koonin, E. V., Dwight, S. S., Harris, M. A., Dolinski, K., Mohr, S., Smith, T., Weng, S., Cherry, J. M. and Botstein, D. (1998) Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282, 2022-2028.
26. Cho, Y. S., Kim, M. K., Cheadle, C., Neary, C., Becker, K. G. and Cho-Chung, Y. S. (2001) Antisense DNAs as multisite genomic modulators identified by DNA microarray. Proc. Natl. Acad. Sci. USA 98, 9819-9823.
27. Cho-Chung, Y. S. and Becker, K. G. (2003) A genome-wide view of antisense. Nat. Biotechnol. 21, 492.
28. Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B. A. and Johnston, M. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71-76.
29. Conlon, I. and Raff, M. (2003) Differences in the way a mammalian cell and yeast cells coordinate cell growth and cell-cycle progression. J. Biol. 2, 7. On-line publication (http:// jbiol.com/content/2/1/7).
30. Cornell, M., Paton, N. W., Hedeler, C., Kirby, P., Delneri, D., Hayes, A. and Oliver, S. G. (2003) GIMS: an integrated data storage and analysis environment for genomic and functional data. Yeast 20, 1291-1306.
31. Costanzo, M. C., Hogan, J. D., Cusick, M. E., Davis, B. P., Fancher, A. M., Hodges, P. E., Kondu, P., Lengieza, C., Lew-Smith, J. E., Lingner, C., Roberg-Perez, K. J., Tillberg, M., Brooks, J. E. and Garrels, J. I. (2000) The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res. 28, 73-76.
32. Cutler, P. (2003) Protein arrays: the current state-of-the-art. Proteomics 3, 3-18.
33. Daniel, J. A., Torok, M. S., Sun, Z. W., Schieltz, D., Allis, C. D., Yates, J. R. and Grant, P. A. (2004) Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription. J. Biol. Chem., in press. doi:10.1074/ jbc.C300494200.
34. Daran-Lapujade, P., Jansen, M. L. A., Daran, J. M., van Gulik, W., de Winde, J. H. and Pronk, J. T. (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae, a chemostat culture study. J. Biol. Chem., in press. doi:10.1074/jbc.M309578200.
35. Delneri, D. and Oliver, S. G. (2000) Functional genomics with yeast; in The Yeast Nucleus: Frontiers in Molecular Biology, Fantes, P. A. and Beggs, J. D. (eds.), pp. 1-18, Oxford University Press. Oxford, UK.
36. Delneri, D., Brancia, F. L. and Oliver, S. G. (2001) Towards a truly integrative biology through the functional genomics of yeast. Curr. Opin. Biotechnol. 12, 87-91.
37. Delneri, D., Colson, I., Grammenoudi, S., Roberts, I. N., Louis, E. J. and Oliver, S. G. (2003) Engineering evolution to study speciation in yeasts. Nature 422, 68-72.
38. Dermitzakis, E. T., Reymond, A., Scamuffa, N., Ucla, C., Kirkness, E., Rossier, C. and Antonarakis, S. E. (2003) Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs) Science 302, 1033-1035.
39. Dillon, N. (2003) Positions, please. Nature 425, 457-458.
40. Dong, L. and Xu, C. W. (2004) Carbohydrates induce monoubiquitination of H2B in yeast. J. Biol. Chem., in press. doi 10.1074/jbc.C300505200.
41. Doniger, S. W., Salomonis, N., Dahlquist, K. D., Vranizan, K., Lawlor, S. C. and Conklin, B. R. (2003) MAPPFinder: using gene ontology and genMAPP to create a global gene-expression profile from microarray data. Genome Biol. 4, R7. On-line publication (http://genomebiology.com/2003/4/1/R7).
42. Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K. and Tuschl, T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498.
43. European Patent Office (2003) EP Patent 1300778. Microarray data warehouse.
44. Fafournoux, P., Bruhat, A. and Jousse, C. (2000) Amino acid regulation of gene expression. Biochem. J. 351, 1-12.
45. Fang, Y., Brass, A., Hoyle, D. C., Hayes, A., Bashein, A., Oliver, S. G., Waddington, D. and Rattray, M. (2003) A model-based analysis of microarray experimental error and normalisation. Nucleic Acids Res. 31, e96.
46. Fernandez-Bellot, E. and Cullin, C. (2001) The protein-only theory and the yeast Saccharomyces cerevisiae: the prions and the propagons. Cell. Mol. Life Sci. 58, 1857-1878.
47. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J., Ross, M. M., Shabanowitz, J., Hunt, D. F. and White, F. M. (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20, 301-305.
48. Fiehn, O. (2001) Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp. Funct. Genomics 2, 155-168.
49. Fiehn, O. (2002) Metabolomics - the link between genotypes and phenotypes. Plant Mol. Biol. 48, 155-171.
50. Fiehn, O. and Weckwerth, W. (2003) Deciphering metabolic networks. Eur. J. Biochem. 270, 579-588.
51. Fiehn, O., Kopka, J., Dormann, P., Altmann, T., Trethewey, R. N. and Willmitzer, L. (2000) Metabolite profiling for plant functional genomics. Nat. Biotechnol. 18, 1157-1161.
52. de la Fuente, A., Brazhnik, P. and Mendes, P. (2002a) Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet. 18, 395-398.
53. de la Fuente, A., Snoep J. E., Westerhoff, H. V. and Mendes, P. (2002b) Metabolic control in integrated biochemical systems. Eur. J. Biochem. 269, 4399-4408.
54. Gancedo, J. M. (1998) Yeast carbon catabolite repression. Microbiol. Mol. Biol. Rev. 62, 334-361.
55. Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D. and Brown, P. O. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell. 11, 4241-4257.
56. Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147.
57. Gavin, A. C. and Superti-Furga, G. (2003) Protein complexes and proteome organization from yeast to man. Curr. Opin. Chem. Biol. 7, 21-27.
58. Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K. and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425, 737-741.
59. Giaever, G., Chu, A. M., Ni, E., Connelly, C., Riles, E., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B. et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391.
60. Glanemann, C., Loos, A., Gorret, N., Willis, L. B., O'Brien, X. M., Lessard, P. A. and Sinskey, A. J. (2003). Disparity between changes in mRNA abundance and enzyme activity in Corynebacterium glutamicum and implications for DNA microarray analysis. Appl. Microbiol. Biotechnol. 61, 61-68.
61. Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M. et al. (1996) Life with 6000 genes. Science 274, 546-567.
62. Goffeau, A., Aert, R., Agostini-Carbone, M. L., Ahmed, A., Aigle, M., Alberghina, L., Albermann, K., Albers, M., Aldea, M., Alexandraki, D., et al. (1997) The yeast genome directory. Nature 387. Suppl. 5, 5-105.
63. Gould, K. L. and Nurse, P. (1989). Tyrosine phosphorylation of the fission yeast cdc2+ protein kinase regulates entry into mitosis. Nature 342, 39-45.
64. Griffin, J. L., Williams, H. J., Sang, E., Clarke, K., Rae, C. and Nicholson, J. K. (2001) Metabolic profiling of genetic disorders: a multitissue (1)H nuclear magnetic resonance spectroscopic and pattern recognition study into dystrophic tissue. Anal. Biochem. 293, 16-21.
65. Grunenfelder, B. and Winzeler, E. A. (2002) Treasures and traps in genome-wide data sets: case examples from yeast. Nature Rev. Genet. 3, 653-661.
66. Guigo, R., Dermitzakis, E. T., Agarwal, P., Ponting, C. P., Parra, G., Reymond, A., Abril, J. F., Keibler, E., Lyle, R., Ucla, C., Antonarakis, S. E. and Brent, M. R. (2003) Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc. Natl. Acad. Sci. USA 100, 1140-1145.
67. Gygi, S. P., Rochon, Y., Franza, B. R. and Aebersold, R. (1999) Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720-1730.
68. Hannon, G. (2002) RNA interference. Nature 418, 244-251.
69. Hansen, J. and Johannesen, P. F. (2000) Cysteine is essential for transcriptional regulation of the sulfur assimilation genes in Saccharomyces cerevisiae. Mol. Gen. Genet. 263, 535-542.
70. Hartwell, L. H. and Weinert, T. A. (1989). Checkpoints: controls that ensure the order of cell cycle events. Science 246, 629-634.
71. Hayes, A., Zhang, N., Wu, J., Butler, P. R., Hauser, N. C., Hoheisel, J. D., Lim, F., Sharrocks, A. D. and Oliver, S. G. (2002) Hybridization array technology coupled with chemostat culture: tools to interrogate gene expression in Saccharomyces cerevisiae. Methods 26, 281-290.
72. Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B. et al. (2004) The HUPO PSI Molecular Interaction Format - A community standard for the representation of protein interaction data. Nature Biotechnology, in press.
73. Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S. L., Millar, A., Taylor, P., Bennett, K., Boutilier, K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183.
74. Howard, K. (2003) Unlocking the money-making potential of RNAi. Nat. Biotechnol. 12, 1441-1446.
75. Howitz, K. T., Bitterman, K. J., Cohen, H. Y., Lamming, D. W., Lavu, S., Wood, J. G., Zipkin, R. E., Chung, P., Kisielewski, A., Zhang, L. L., Scherer, B. and Sinclair, D. A. (2003) Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan. Nature 425, 191-196.
76. Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R., Armour, C. D., Bennett, H. A., Coffey, E., Dai, H., He, Y. D. et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102, 109-126.
77. Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S. and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast. Nature 425, 686-691.
78. Ihmels, J., Levy, R. and Barkai, N. (2004) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat. Biotechnol., in press. doi:10.1038/nbt918.
79. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. and Sakaki, Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA. 98, 4569-4574.
80. Kamath, R. S., Fraser, A. G., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., Welchman, D. P., Zipperlen, P. and Ahringer, J. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231-237.
81. Kell, D. B. and King, R. D. (2000) On the optimization of classes for the assignment of unidentified reading frames in functional genomics programmes: the need for machine learning. Trends Biotechnol. 18, 93-98.
82. Kell, D. B. and Mendes, P. (2000) Snapshots of systems: metabolic control analysis and biotechnology in the post-genomic era; in Technological and Medical Implications of Metabolic Control Analysis, Cornish-Bowden, A. and Cardenas, M. L. (eds.), pp. 3-25, Kluwer Academic Publishers, Dordrecht, Netherlands.
83. Kellis, M., Patterson, N., Endrizzi, M., Birren, B. and Lander, E. S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254.
84. Kitano, H. (2002) Systems biology: a brief overview. Science 295, 1662-1664.
85. Knight, Z. A., Schilling, B., Row, R. H., Kenski, D. M., Gibson, B. W. and Shokat, K. M. (2003) Phosphospecific proteolysis for mapping sites of protein phosphorylation. Nat. Biotechnol. 21, 1047-1054.
86. Kodadek, T. (2001) Protein microarrays: prospects and problems. Chem. Biol. 8, 105-115.
87. Kryndushkin, D. S., Alexandrov, I. M., Ter-Avanesyan, M. D. and Kushnirov, V. V. (2003) Yeast [PSI+] prion aggregates are formed by small Sup35 polymers fragmented by Hsp104. J. Biol. Chem. 278, 49636-49643.
88. Kuhn, A. N. and Käufer, N. F. (2003) Pre-mRNA splicing in Schizosaccharomyces pombe. Regulatory role of a kinase conserved from fission yeast to mammals. Curr. Genet. 42, 241-251.
89. Kumar, A., Harrison, P. M., Cheung, K-H., Lan, N., Echols, N., Bertone, P., Miller, P., Gerstein, M. B. and Snyder, M. (2002) An integrated approach for finding overlooked genes in yeast. Nat. Biotechnol. 20, 58-63.
90. Lal, S. P., Christopherson, R. I. and dos Remedios, C. G. (2002) Antibody arrays: an embryonic but rapidly growing technology. Drug Discov. Today 7, S143-S149.
91. Lane, P. G., Oliver, S. G. and Butler, P. R. (1999) Analysis of a continuous-culture technique for the selection of mutants tolerant to extreme environmental stress. Biotechnol. Bioeng. 65, 397-406.
92. Lashkari, D. A., DeRisi, J. L., McCusker, J. H., Namath, A. F., Gentile, C., Hwang, S. Y., Brown, P. O. and Davis, R. W. (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl. Acad. Sci. USA 94, 13057-13062.
93. Lasko, D. R., Zamboni, N. and Sauer, U. (2000) Bacterial response to acetate challenge: a comparison of tolerance amomg species. Appl. Microbiol. Biotechnol. 54, 243-247.
94. Lee, J. H., Lee, D. E., Lee, B. U. and Kim, H. S. (2003a) Global analyses of transcriptomes and proteomes of a parent strain and an L-threonine-overproducing mutant strain. J. Bacteriol. 185, 5442-5451.
95. Lee, D. Y., Yun, H., Park, S. and Lee, S. Y. (2003b) MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics 19, 2144-2146.
96. Levine, M. and Tjian, R. (2003) Transcriptional regulation and animal diversity. Nature 424, 147-151.
97. Levy-Lahad, E. and Plon, S. E. (2003) A risky business. Assessing breast cancer risk. Science 302, 574-575.
98. Liang, P. and Pardee, A. B. (2003) Analysing differential gene expression in cancer. Nat. Rev. Cancer 3, 869-876.
99. Lidstrom, M. and Meldrum, D. R. (2003) Life on a chip. Nat. Rev. Microbiol. 1, 158-164.
100. Lim, F. L., Hayes, A., West, A. G., Pic-Taylor, A., Morgan, B. A., Oliver, S. G. and Sharrocks, A. D. (2003) Mcm1p-induced DNA bending regulates the formation of ternary transcription factor complexes. Mol. Cell. Biol. 23, 450-461.
101. Lipford, J. R. and Deshaies, R. J. (2003) Diverse roles for ubiquitin-dependent proteolysis in transcriptional activation. Nat. Cell Biol. 10, 845-850.
102. Mendes, P. (2002) Emerging bioinformatics for the metabolome. Brief. Bioinformatics 3, 134-145.
103. Michaud, G. A., Salcius, M., Zhou, F., Bangham, R., Bonin, J., Guo, H., Snyder, M., Predki, P. F. and Schweitzer, B. I. (2003) Analyzing antibody specificity with whole proteome microarrays. Nat. Biotechnol. 21, 1509-1512.
104. Mitchell, P. (2002) A perspective on protein microarrays. Nat. Biotechnol. 20, 225-229.
105. Morange, M. (2002) The misunderstood gene. Harvard University Press. Cambridge, USA.
106. Mosley, A. L., Lakshmanan, J., Aryal, B. K. and Ozcan, S. (2003) Glucose-mediated phosphorylation converts the transcription factor Rgt1 from a repressor to an activator. J. Biol. Chem. 278, 10322-10327.
107. Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562.
108. Muller, D., Exler, S., Aguilera-Vazquez, L., Guerrero-Martin, E. and Reuss, M. (2003) Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae. Yeast 20, 351-367.
109. Muratani, M. and Tansey, W. P. (2003) How the ubiquitin-proteasome system controls transcription. Nat. Rev. Mol. Cell. Biol. 4, 192-201.
110. Oliver, D. J., Nikolau, B. J. and Wurtele, E. S. (2002) Functional Genomics: High-throughput mRNA, protein, and metabolite analyses. Metabolic engineering 4, 98-108.
111. Oliver, S. G. (1996) From DNA sequence to biological function. Nature 379, 597-600.
112. Oliver, S. G. (1997) Yeast as a navigational aid in genome analysis. Microbiology 143, 1483-1487.
113. Oliver, S. G. (1998) Introduction to functional analysis of the yeast genome. Methods in Microbiology 26, 1-13.
114. Oliver, S. G. (2002) Functional genomics: lessons from yeast. Philos. Trans. Roy. Soc. B., 357, 17-23.
115. Oliver, S. G., Winson, M. K., Kell, D. B. and Baganz, F. (1998) Systematic functional analysis of the yeast genome. Trends Biotechnol. 16, 373-378.
116. Orchard, S., Hermjakob, H. and Apweiler, R. (2003) The proteomics standards initiative. Proteomics 3, 1374-1376.
117. Outeiro, T. F. and Lindquist S. (2003) Yeast cells provide insight into alpha-synuclein biology and pathobiology. Science 302, 1772-1775.
118. Ouyang, Z., Takats, Z., Blake, T. A., Gologan, B., Guymon, A. J., Wiseman, J. M., Oliver, J. C., Davisson, V. J. and Cooks, R. G. (2003) Preparing protein microarrays by soft-landing of mass-selected ions. Science 301, 1351-1354.
119. Payne, W. E. and Garrels, J. I. (1997). Yeast protein database (YPD): a database for the complete proteome of Saccharomyces cerevisiae. Nucleic Acids Res. 25, 57-62. (http://www.incyte.com/control/researchproducts/insilico/ proteome).
120. Pearson, H. (2003) Geneticists play the numbers game in vain. Nature 423, 576.
121. Peri, S., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K., Gronborg, M. et al. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 13, 2363-2371.
122. Phelps, T. J., Palumbo, A. V. and Beliaev, A. S. (2002) Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. Curr. Opin. Biotechnol. 13, 20-24.
123. Pratt, J. M., Petty, J., Riba-Garcia, I., Robertson, D. H. L., Gaskell, S. J., Oliver, S. G. and Beynon, R. J. (2002) Dynamics of protein turnover, a missing dimension in proteomics. Mol. Cell Proteomics 1, 579-591.
124. Raamsdonk, L. M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M. C., Berden, J. A., Brindle, K. M., Kell, D. B., Rowland, J. J., Westerhoff, H. V., van Dam, K. and Oliver, S. G. (2001) A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol. 19, 45-50.
125. Raponi, M. and Arndt, G. M. (2003) Double-stranded RNA-mediated gene silencing in fission yeast. Nucleic Acids Res. 31, 4481-4489.
126. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M. and Seraphin, B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol. 17, 1030-1032.
127. Rohde, J. R. and Cardenas, M. E. (2003) The tor pathway regulates gene expression by linking nutrient sensing to histone acetylation. Mol. Cell. Biol. 23, 629-635.
128. Rose, A. H. and Harrison, J. S. (1987-1995) The yeasts. Vol. 1-6. Academic Press, London, UK.
129. Ross-Macdonald, P., Coelho, P. S., Roemer, T., Agarwal, S., Kumar, A., Jansen, R., Cheung, K. H., Sheehan, A., Symoniatis, D., Umansky, L. et al. (1999) Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402, 413-418.
130. Salzberg, S. L. (2003) Genomics: Yeast rises again. Nature 423, 233-234.
131. Sandelin, A., Hoglund, A., Lenhard, B. and Wasserman, W. W. (2003) Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Funct. Integr. Genomics 3, 125-134.
132. Schena, M., Shalon, D., Davis, R. W. and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470.
133. Scherer, L. J. and Rossi, J. J. (2003) Approaches for the sequence-specific knockdown of mRNA. Nat. Biotechnol. 21, 1457-1465.
134. Schramke, V. and Allshire, R. (2003) Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301, 1069-1074.
135. Sherman, M. Y. and Muchowski, P. J. (2003) Making yeast tremble: yeast models as tools to study neurodegenerative disorders. Neuromolecular Med. 4, 133-146.
136. Shiio, Y. and Eisenman, R. N. (2003) Histone sumoylation is associated with transcriptional repression. Proc. Natl. Acad. Sci. USA 100, 13225-13230.
137. Shoemaker, D. D., Schadt, E. E., Armour, C. D., He, Y. D., Garrett-Engele, P., McDonagh, P. D., Loerch, P. M., Leonardson, A., Lum, P. Y., Cavet, G. et al. (2001) Experimental annotation of the human genome using microarray technology. Nature 409, 922-927.
138. So, E. N. and Crowe, D. L. (2000) Characterization of a retinoic acid responsive element in the human ets-1 promoter. IUBMB Life 50, 365-370.
139. Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D. and Futcher, B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297.
140. Spruill, S., Hardy, S., Weir, B. S., and Lu, J. (2002) Assessing sources of variability in microarray gene expression data. BioTechniques 33, 916-923.
141. Tate, J. J. and Cooper, T. G. (2003) Tor1/2 regulation of retrograde gene expression in Saccharomyces cerevisiae derives indirectly as a consequence of alterations in ammonia metabolism. J. Biol. Chem. 278, 36924-36933.
142. Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D., Stead, D. A., Yin, Z., Deutsch, E. W., Selway, L., Walker, J., RibaGarcia, I. et al. (2003) A systematic approach to modelling capturing and disseminating proteomics experimental data. Nat. Biotechnol. 21, 247-254.
143. ter Kuile, B. H. (1999) Regulation and adaptation of glucose metabolism of the parasitic protist Leishmania donovani at the enzyme and mRNA levels. J. Bacteriol. 181, 4863-4872.
144. ter Kuile, B. H. and Westerhoff, H. V. (2001) Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett. 500, 169-171.
145. ter Linde, J. J., Liang, H., Davis, R. W., Steensma, H. Y., van Dijken, J. P. and Pronk, J. T. (1999) Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae. J. Bacteriol. 181, 7409-7413.
146. Teusink, B., Baganz, F., Westerhoff, H. V. and Oliver, S. G. (1998) Metabolic control analysis as a tool in the elucidation of the function of novel genes. Methods Microbiol. 26, 297-336.
147. The Caenorhabditis elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282, 2012-2018.
148. The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I & II Team (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563-573.
149. The International Human Genome Mapping Consortium (2001a) Initial sequencing and analysis of the human genome. Nature 409, 860-921.
150. The International Human Genome Mapping Consortium (2001b) A physical map of the human genome. Nature 409, 934-941.
151. th April 2003) (http://www.genome.gov/11006929; http://www. sanger.ac.uk/Info/Press/2003/ 030414.shtml).
152. Tilstone, C. (2003) Vital statistics. Nature 424, 610-613.
153. Trethewey, R. N. (2001) Gene discovery via metabolic profiling. Curr. Opin. Biotechnol. 12, 135-138.
154. Trethewey, R. N., Krotzky, A. I. and Willmitzer, L. (1999) Metabolic profiling: a Rosetta stone for genomics? Curr. Opin. Plant Biol. 2, 83-85.
155. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627.
156. Urbanczyk-Wochniak, E., Luedemann, A., Kopka, J., Selbig, J., Roessner-Tunali, U., Willmitzer, L. and Fernie, A. R. (2003) Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep. 4, 989-993.
157. US Patent Office (2003) US Patent 6544742. Detection of genes regulated by EGF in breast cancer.
158. US Patent Office (2003) US Patent 2003124581. Newborn screening for hemoglobinopathy by DNA microarray analysis.
159. US Patent Office (2003) US Patent 2003170672. Quality control method of DNA microarray.
160. US Patent Office (2003) US Patent 2003180774. Exploiting genomes in the search for new drugs.
161. US Patent Office (2003) US Patent 2003180800. Stable isotope based dynamic metabolic profiling of living organisms for characterization of metabolic diseases, drug testing and drug development.
162. Verger, A., Perdomo, J. and Crossley, M. (2003) Modification with SUMO. A role in transcriptional regulation. EMBO Rep. 4, 137-142.
163. Volpe, T., Schramke, V., Hamilton, G. L., White, S. A., Teng, G., Martienssen, R. A. and Allshire, R. C. (2003) RNA interference is required for normal centromere function in fission yeast. Chromosome Res. 11, 137-146.
164. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S. and Bork, P. (2002) Comparative assessment of large-scale data sets of proteinprotein interactions. Nature 417, 399-403.
165. Walker, G. M. (1999) Synchronization of yeast cell populations. Methods Cell Sci. 21, 87-93.
166. Warringer, J. and Blomberg, A. (2003) Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae. Yeast 20, 53-67.
167. Washburn, M. P. (2003) Soft landing for protein chips. Nat. Biotechnol. 21, 1156-1157.
168. Watkins, S. M. and German, J. B. (2002) Metabolomics and biochemical profiling in drug discovery and development. Curr. Opin. Mol. Ther. 4, 224-228.
169. Weckwerth, W. (2003) Metabolomics in systems biology. Annu. Rev. Plant Biol. 54, 669-689.
170. Weckwerth, W. and Fiehn, O. (2002) Can we discover novel pathways using metabolomic analysis? Curr. Opin. Biotechnol. 13, 156-160.
171. Weusthuis, R. A., Pronk, J. T., van den Broek, P. J. and van Dijken, J. P. (1994) Chemostat cultivation as a tool for studies on sugar transport in yeasts. Microbiol. Rev. 58, 616-630.
172. Willingham, S., Outeiro, T. F., DeVit, M. J., Lindquist, S. L. and Muchowski, P. J. (2003) Yeast genes that enhance the toxicity of a mutant huntingtin fragment or α-synuclein. Science 302, 1769-1772.
173. Winzeler, E. A., Shoemaker, D. D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J. D., Bussey, H. et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906.
174. Wodicka, L., Dong, H., Mittmann, M., Ho, M. H. and Lockhart, D. J. (1997) Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotechnol. 15, 1359-1367.
175. Wohlschlegel, J. A. and Yates, J. R. (2003) Proteomics: Wheres Waldo in yeast? Nat. 425, 671-672.
176. Wood, V., Gwilliam, R., Rajandream, M. A., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J., Baker, S. et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415, 871-880.
177. World Intellectual Property Organisation (1999) WO Patent 9957306. Method for diagnosing a vascular condition.
178. World Intellectual Property Organisation (2001) WO Patent 0140896. System and method for metabolic profiling.
179. World Intellectual Property Organisation (2001) WO Patent 0178652. Methods for drug discovery, disease treatment and diagnosis using metabolomics.
180. World Intellectual Property Organisation (2001) WO Patent 0194946. Microarrays for performing proteomic analyses.
181. World Intellectual Property Organisation (2002) WO Patent 02057989. Metabolome profiling methods using chromatographic and spectroscopic data in pattern recognition analysis.
182. World Intellectual Property Organisation (2002) WO Patent 02092118. Global analysis of protein activities using proteome chips.
183. World Intellectual Property Organisation (2002) WO Patent 0218646. Gene discovery using microarrays.
184. World Intellectual Property Organisation (2002) WO Patent 0239120. Method for identifying the proteome of cells using an antibody library microarray.
185. World Intellectual Property Organisation (2003) WO Patent 03025213. Yeast proteome analysis.
186. World Intellectual Property Organisation (2003) WO Patent 03058238. Combined metabolomic, proteomic and transcriptomic analysis from one, single sample and suitable statistical evaluation data.
187. World Intellectual Property Organisation (2003) WO Patent 03070918. RNA interference mediated inhibition of gene expression using chemically modified short interfering nucleic acid.
188. World Intellectual Property Organisation (2003) WO Patent 03087371. Antiviral therapy on the basis of RNA interference.
189. Wu, L. F., Hughes, T. R., Davierwala, A. P., Robinson, M. D., Stoughton, R. and Altschuler S. J. (2002) Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet. 31, 255-265.
190. Yamada, K., Lim, J., Dale, J. M., Chen, H., Shinn, P., Palm, C. J., Southwick, A. M., Wu, H. C., Kim, C., Nguyen, M. et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302, 842-846.
191. Yao, T. (2002) Bioinformatics for the genomic sciences and towards systems biology. Japanese activities in the post-genome era. Prog. Biophys. Mol. Biol. 80, 23-42.
192. Zeng, Q., Morales, A. J. and Cottarel, G. (2001) Fungi and humans: closer than you think. Trends Genet. 17, 682-684.
193. Zhang, N., Osborn, M., Gitsham, P., Yen, K., Miller, J. R. and Oliver, S. G. (2003) Using yeast to place human genes in functional categories. Gene 303, 121-129.
194. Zhu, H. and Snyder, M. (2003) Protein chip technology. Curr. Opin. Chem. Biol. 7, 55-63.
195. Zhu, H., Bilgin, M. and Snyder, M. (2003) Proteomics. Annu. Rev. Biochem. 72, 783-812.
196. 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, R. A., Gerstein, M. and Snyder, M. (2001) Global analysis of protein activities using proteome chips. Science 293, 2101-2105.