Functional genomics and proteomics: Charting a multidimensional map of the yeast cell

Trends in Cell Biology

Volumn 13, Issue 7, 2003, Pages 344-356

  Bader, Gary D ^a   Heilbut, Adrian ^b   Andrews, Brenda ^c   Tyers, Mike ^c,d   Hughes, Timothy ^c   Boone, Charles ^c  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b MDS Proteomics Inc   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d MOUNT SINAI HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ANALYTIC METHOD; BIOINFORMATICS; BIOTECHNOLOGY; CROSS LINKING; CRYSTAL STRUCTURE; CYTOLOGY; DATA ANALYSIS; DNA MICROARRAY; FUNGAL GENETICS; GENE DELETION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE INTERACTION; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENE STRUCTURE; GENE TECHNOLOGY; GENETIC CODE; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GENOMICS; MOLECULAR INTERACTION; PHENOTYPE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION; VALIDATION PROCESS; YEAST CELL;

FUNGI; MYXOGASTRIA; SACCHAROMYCETALES;

EID: 0037756723     PISSN: 09628924     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0962-8924(03)00127-2     Document Type: Review

References (138)

1. Fields S. Proteomics. Proteomics in genomeland. Science. 291:2001;1221-1224.
2. Fields S., Johnston M. Genomics. A crisis in postgenomic nomenclature. Science. 296:2002;671-672.
3. Steven W.H., et al. Computational modeling of the EGF-receptor system: a paradigm for systems biology. Trends Cell Biol. 13:2003;43-50.
4. Covert M.W., et al. Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26:2001;179-186.
5. Cross F.R., et al. Testing a mathematical model of the yeast cell cycle. Mol. Biol. Cell. 13:2002;52-70.
6. Hartwell L.H., et al. From molecular to modular cell biology. Nature. 402:1999;C47-C52.
7. Ideker T., et al. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2:2001;343-372.
8. Levsky J.M., Singer R.H. Gene expression and the myth of the average cell. Trends Cell Biol. 13:2003;4-6.
9. Grunenfelder B., Winzeler E.A. Treasures and traps in genome-wide data sets: case examples from yeast. Nat. Rev. Genet. 3:2002;653-661.
10. Oliver S.G., et al. The complete DNA sequence of yeast chromosome III. Nature. 357:1992;38-46.
11. Goffeau A., et al. Life with 6000 genes. Science. 274, 546:1996;563-567.
12. Bader G.D., et al. BIND - the Biomolecular Interaction Network Database. Nucleic Acids Res. 29:2001;242-245.
13. Xenarios I., et al. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30:2002;303-305.
14. Zanzoni A., et al. MINT: a Molecular INTeraction database. FEBS Lett. 513:2002;135-140.
15. Breitkreutz B.J., et al. The GRID: the general repository for interaction datasets. Genome Biol. 3:2002;R0013.
16. Mewes H.W., et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 30:2002;31-34.
17. Dwight S.S., et al. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30:2002;69-72.
18. von Mering C., et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 417:2002;399-403.
19. Bader G.D., Hogue C.W. Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol. 20:2002;991-997.
20. Lee T.I., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 298:2002;799-804.
21. Horak C.E., et al. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev. 16:2002;3017-3033.
22. Iyer V.R., et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 409:2001;533-538.
23. Tong A.H., et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 294:2001;2364-2368.
24. Endy D., Brent R. Modelling cellular behaviour. Nature. 409:(Suppl.):2001;391-395.
25. Edwards J.S., Palsson B.O. Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics. 1:2000;1.
26. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
27. Venter J.C., et al. The sequence of the human genome. Science. 291:2001;1304-1351.
28. Benson D.A., et al. GenBank. Nucleic Acids Res. 30:2002;17-20.
29. Overbeek R., et al. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28:2000;123-125.
30. Paley S.M., Karp P.D. Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics. 18:2002;715-724.
31. Mathe C., et al. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res. 30:2002;4103-4117.
32. Cliften P.F., et al. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 11:2001;1175-1186.
33. Kumar A., et al. An integrated approach for finding overlooked genes in yeast. Nat. Biotechnol. 20:2002;58-63.
34. Shoemaker D.D., et al. Experimental annotation of the human genome using microarray technology. Nature. 409:2001;922-927.
35. Lipton M.S., et al. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc. Natl. Acad. Sci. U. S. A. 99:2002;11049-11054.
36. Ho Y., et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 415:2002;180-183.
37. Vaglio P., et al. WorfDB: the Caenorhabditis elegans ORFeome Database. Nucleic Acids Res. 31:2003;237-240.
38. Paigen K., Eppig J.T. A mouse phenome project. Mamm. Genome. 11:2000;715-717.
39. Winzeler E.A., et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 285:1999;901-906.
40. Chang M., et al. A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage. Proc. Natl. Acad. Sci. U. S. A. 99:2002;16934-16939.
41. Jorgensen P., et al. Systematic identification of pathways that couple cell growth and division in yeast. Science. 297:2002;395-400.
42. Giaever G., et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418:2002;387-391.
43. Page N., et al. A Saccharomyces cerevisiae genome-wide mutant screen for altered sensitivity to K1 killer toxin. Genetics. 163:2003;875-894.
44. Ni L., Snyder M. A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol. Biol. Cell. 12:2001;2147-2170.
45. Bonangelino C.J., et al. Genomic screen for vacuolar protein sorting genes in Saccharomyces cerevisiae. Mol. Biol. Cell. 13:2002;2486-2501.
46. Jiang B., et al. Novel strategies in antifungal lead discovery. Curr. Opin. Microbiol. 5:2002;466-471.
47. Steinmetz L.M., et al. Systematic screen for human disease genes in yeast. Nat. Genet. 31:2002;400-404.
48. Piano F., et al. RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans. Curr. Biol. 10:2000;1619-1622.
49. Kamath R.S., et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature. 421:2003;231-237.
50. Hudson D.F., et al. Reverse genetics of essential genes in tissue-culture cells: 'dead cells talking'. Trends Cell Biol. 12:2002;281-287.
51. Nolan P.M., et al. A systematic, genome-wide, phenotype-driven mutagenesis programme for gene function studies in the mouse. Nat. Genet. 25:2000;440-443.
52. Wu R.Z., et al. Cell-biological applications of transfected-cell microarrays. Trends Cell Biol. 12:2002;485-488.
53. Kononen J., et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med. 4:1998;844-847.
54. Schena M., et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270:1995;467-470.
55. Packer, A. (ed.) (2002) Nature Genetics Chipping Forecast II. Nat. Genet. 32 (Suppl.), 461-552.
56. Hughes T.R., et al. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19:2001;342-347.
57. Nuwaysir E.F., et al. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12:2002;1749-1755.
58. Ashby, M. and Rine, J. (10-29-1996) Methods for drug screening. The Regents of the University of California. Oakland, CA. USA., Patent number: 5,569,588.
59. Ideker T., et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 292:2001;929-934.
60. Grigoriev A. A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 29:2001;3513-3519.
61. Ge H., et al. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet. 29:2001;482-486.
62. Jansen R., et al. Relating whole-genome expression data with protein-protein interactions. Genome Res. 12:2002;37-46.
63. Eisen M.B., et al. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. U. S. A. 95:1998;14863-14868.
64. Wu L.F., et al. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet. 31:2002;255-265.
65. Hughes T.R., et al. Functional discovery via a compendium of expression profiles. Cell. 102:2000;109-126.
66. Tavazoie S., et al. Systematic determination of genetic network architecture. Nat. Genet. 22:1999;281-285.
67. Horak C.E., Snyder M. ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol. 350:2002;469-483.
68. Robyr D., et al. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell. 109:2002;437-446.
69. van Leeuwen F., et al. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell. 109:2002;745-756.
70. Tanaka T., Nasmyth K. Association of RPA with chromosomal replication origins requires an Mcm protein, and is regulated by Rad53, and cyclin- and Dbf4-dependent kinases. EMBO J. 17:1998;5182-5191.
71. Blat Y., Kleckner N. Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region. Cell. 98:1999;249-259.
72. Pe'er D., et al. Inferring subnetworks from perturbed expression profiles. Bioinformatics. 17:(Suppl. 1):2001;S215-S224.
73. Ronen M., et al. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. U. S. A. 99:2002;10555-10560.
74. Ideker T., et al. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 18:(Suppl. 1):2002;S233-S240.
75. Uetz P., et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:2000;623-627.
76. Uetz P. Two-hybrid arrays. Curr. Opin. Chem. Biol. 6:2002;57-62.
77. Ito T., et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U. S. A. 98:2001;4569-4574.
78. Gavin A.C., et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:2002;141-147.
79. Tong A.H., et al. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science. 295:2002;321-324.
80. Remy I., et al. Detection and visualization of protein interactions with protein fragment complementation assays. Methods Mol. Biol. 185:2002;447-459.
81. Edwards A., et al. Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet. 18:2002;529.
82. Kemmeren P., et al. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol. Cell. 9:2002;1133-1143.
83. Schwikowski B., et al. A network of protein-protein interactions in yeast. Nat. Biotechnol. 18:2000;1257-1261.
84. Albert R., et al. Error and attack tolerance of complex networks. Nature. 406:2000;378-382.
85. Gerstein M., et al. Proteomics. Integrating interactomes. Science. 295:2002;284-287.
86. Deane C.M., et al. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol. Cell Proteomics. 1:2002;349-356.
87. Bader G.D., Hogue C.W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 4:2003;2.
88. Gaasterland T., Bekiranov S. Making the most of microarray data. Nat. Genet. 24:2000;204-206.
89. Bock J.R., Gough D.A. Predicting protein-protein interactions from primary structure. Bioinformatics. 17:2001;455-460.
90. Guarente L. Synthetic enhancement in gene interaction: a genetic tool come of age. Trends Genet. 9:1993;362-366.
91. Novick P., et al. Suppressors of yeast actin mutations. Genetics. 121:1989;659-674.
92. Forsburg S.L. The art and design of genetic screens: yeast. Nat. Rev. Genet. 2:2001;659-668.
93. Hartman J.L., et al. Principles for the buffering of genetic variation. Science. 291:2001;1001-1004.
94. Kumar A., et al. Subcellular localization of the yeast proteome. Genes Dev. 16:2002;707-719.
95. Gene ontology: tool for the unification of biology. Nat. Genet. 25:2000;25-29.
96. Shimada Y., et al. Nuclear sequestration of the exchange factor Cdc24 by Far1 regulates cell polarity during yeast mating. Nat. Cell Biol. 2:2000;117-124.
97. Medalia O., et al. Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science. 298:2002;1209-1213.
98. Mann M., et al. Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70:2001;437-473.
99. Andersen J.S., et al. Directed proteomic analysis of the human nucleolus. Curr. Biol. 12:2002;1-11.
100. Smolka M., et al. Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol. Cell Proteomics. 1:2002;19-29.
101. Dimster-Denk D., et al. Comprehensive evaluation of isoprenoid biosynthesis regulation in Saccharomyces cerevisiae utilizing the genome reporter matrix. J. Lipid Res. 40:1999;850-860.
102. Oda Y., et al. Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nat. Biotechnol. 19:2001;379-382.
103. Ficarro S.B., et al. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20:2002;301-305.
104. Wells L., et al. Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications. Mol. Cell Proteomics. 1:2002;791-804.
105. Mann M., et al. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol. 20:2002;261-268.
106. Grayhack E.J., Phizicky E.M. Genomic analysis of biochemical function. Curr. Opin. Chem. Biol. 5:2001;34-39.
107. Christendat D., et al. Structural proteomics of an archaeon. Nat. Struct. Biol. 7:2000;903-909.
108. Stevens R.C., et al. Global efforts in structural genomics. Science. 294:2001;89-92.
109. Montelione G.T. Structural genomics: an approach to the protein folding problem. Proc. Natl. Acad. Sci. U. S. A. 98:2001;13488-13489.
110. Dyson H.J., Wright P.E. Coupling of folding and binding for unstructured proteins. Curr. Opin. Struct. Biol. 12:2002;54-60.
111. Pieper U., et al. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 30:2002;255-259.
112. Vitkup D., et al. Completeness in structural genomics. Nat. Struct. Biol. 8:2001;559-566.
113. Martzen M.R., et al. A biochemical genomics approach for identifying genes by the activity of their products. Science. 286:1999;1153-1155.
114. Zhu H., et al. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26:2000;283-289.
115. Slepchenko B.M., et al. Computational cell biology: spatiotemporal simulation of cellular events. Annu. Rev. Biophys. Biomol. Struct. 31:2002;423-441.
116. Gasch A.P., et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell. 11:2000;4241-4257.
117. Dragon F., et al. A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature. 417:2002;967-970.
118. Fatica A., Tollervey D. Making ribosomes. Curr. Opin. Cell Biol. 14:2002;313-318.
119. Jeong H., et al. Lethality and centrality in protein networks. Nature. 411:2001;41-42.
120. Wagner A. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18:2001;1283-1292.
121. Gilman A.G., et al. Overview of the alliance for cellular signaling. Nature. 420:2002;703-706.
122. Walhout A.J., et al. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr. Biol. 12:2002;1952-1958.
123. Vidal M. A biological atlas of functional maps. Cell. 104:2001;333-339.
124. Edgar R., et al. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30:2002;207-210.
125. Gollub J., et al. The Stanford microarray database: data access and quality assessment tools. Nucleic Acids Res. 31:2003;94-96.
126. Matys V., et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31:2003;374-378.
127. Karp P.D., et al. The EcoCyc database. Nucleic Acids Res. 30:2002;56-58.
128. van Helden J., et al. From molecular activities and processes to biological function. Brief. Bioinform. 2:2001;81-93.
129. Ananko E.A., et al. GeneNet: a database on structure and functional organisation of gene networks. Nucleic Acids Res. 30:2002;398-401.
130. Michalickova K., et al. SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics. 3:2002;32.
131. Stein L. Creating a bioinformatics nation. Nature. 417:2002;119-120.
132. Furey T.S., et al. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics. 16:2000;906-914.
133. Drawid A., Gerstein M. A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. J. Mol. Biol. 301:2000;1059-1075.
134. Bertone P., et al. SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Res. 29:2001;2884-2898.
135. Breitkreutz B.J., et al. Osprey: a network visualization system. Genome Biol. 3:2002;R0012.
136. Enright A.J., Ouzounis C.A. BioLayout - an automatic graph layout algorithm for similarity visualization. Bioinformatics. 17:2001;853-854.
137. Roberts C.J., et al. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science. 287:2000;873-880.
138. Greenbaum D., et al. Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Genome Res. 11:2001;1463-1468.