Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

Journal of Biology

Volumn 5, Issue , 2006, Pages

  Reguly, Teresa ^a   Breitkreutz, Ashton ^a   Boucher, Lorrie ^a,b   Breitkreutz, Bobby Joe ^a   Hon, Gary C ^c   Myers, Chad L ^d,e   Parsons, Ainslie ^b,f   Friesen, Helena ^f   Oughtred, Rose ^d   Tong, Amy ^b,f   Stark, Chris ^a   Ho, Yuen ^f   Botstein, David ^d   Andrews, Brenda ^b,f   Boone, Charles ^b,f   Troyanskya, Olga G ^d,e   Ideker, Trey ^c   Dolinski, Kara ^d   Batada, Nizar N ^a   Tyers, Mike ^a,b  

^a MOUNT SINAI HOSPITAL   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d PRINCETON UNIVERSITY   (United States)

^e Princeton University   (United States)

^f UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BUDDING; COMPUTER NETWORK; FUNGAL GENE; GENE INTERACTION; GENETIC DATABASE; GENOME ANALYSIS; MEDICAL LITERATURE; PREDICTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; BIOLOGY; GENETICS; METABOLISM; PROTEIN ANALYSIS;

SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

SACCHAROMYCES CEREVISIAE PROTEIN;

COMPUTATIONAL BIOLOGY; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 33847064282     PISSN: 14785854     EISSN: 14754924     Source Type: Journal    
DOI: 10.1186/jbiol36     Document Type: Article

References (110)

1. Transcriptional networks: reverse-engineering gene regulation on a global scale. G Chua MD Robinson Q Morris TR Hughes, Curr Opin Microbiol 2004 7 638 646 10.1016/j.mib.2004.10.009 15556037
2. Functional profiling of the Saccharomyces cerevisiae genome. G Giaever AM Chu L Ni C Connelly L Riles S Veronneau S Dow A Lucau-Danila K Anderson B Andre, Nature 2002 418 387 391 10.1038/nature00935 12140549
3. Functional genomics and proteomics: charting a multidimensional map of the yeast cell. GD Bader A Heilbut B Andrews M Tyers T Hughes C Boone, Trends Cell Biol 2003 13 344 356 10.1016/S0962-8924(03)00127-2 12837605
4. Harvesting the genome's bounty: integrative genomics. P Jorgensen BJ Breitkreutz K Breitkreutz C Stark G Liu M Cook J Sharom JL Nishikawa T Ketela D Bellows, Cold Spring Harb Symp Quant Biol 2003 68 431 443 10.1101/sqb.2003.68. 431 15338646
5. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. P Uetz L Giot G Cagney TA Mansfield RS Judson JR Knight D Lockshon V Narayan M Srinivasan P Pochart, Nature 2000 403 623 627 10.1038/35001009 10688190
6. 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. T Ito K Tashiro S Muta R Ozawa T Chiba M Nishizawa K Yamamoto S Kuhara Y Sakaki, Proc Natl Acad Sci USA 2000 97 1143 1147 10655498 10.1073/pnas.97.3.1143
7. A comprehensive two-hybrid analysis to explore the yeast protein interactome. T Ito T Chiba R Ozawa M Yoshida M Hattori Y Sakaki, Proc Natl Acad Sci USA 2001 98 4569 4574 11283351 10.1073/pnas.061034498
8. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Y Ho A Gruhler A Heilbut GD Bader L Moore SL Adams A Millar P Taylor K Bennett K Boutilier, Nature 2002 415 180 183 10.1038/415180a 11805837
9. Functional organization of the yeast proteome by systematic analysis of protein complexes. AC Gavin M Bosche R Krause P Grandi M Marzioch A Bauer J Schultz JM Rick AM Michon CM Cruciat, Nature 2002 415 141 147 10.1038/415141a 11805826
10. Systematic genetic analysis with ordered arrays of yeast deletion mutants. AH Tong M Evangelista AB Parsons H Xu GD Bader N Page M Robinson S Raghibizadeh CW Hogue H Bussey, Science 2001 294 2364 2368 10.1126/science. 1065810 11743205
11. DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. SL Ooi DD Shoemaker JD Boeke, Nat Genet 2003 35 277 286 10.1038/ng1258 14566339
12. Global mapping of the yeast genetic interaction network. AH Tong G Lesage GD Bader H Ding H Xu X Xin J Young GF Berriz RL Brost M Chang, Science 2004 303 808 813 10.1126/science.1091317 14764870
13. A robust toolkit for functional profiling of the yeast genome. X Pan DS Yuan D Xiang X Wang S Sookhai-Mahadeo JS Bader P Hieter F Spencer JD Boeke, Mol Cell 2004 16 487 496 10.1016/j.molcel.2004.09.035 15525520
14. A protein interaction map of Drosophila melanogaster. L Giot JS Bader C Brouwer A Chaudhuri B Kuang Y Li YL Hao CE Ooi B Godwin E Vitols, Science 2003 302 1727 1736 10.1126/science.1090289 14605208
15. A map of the interactome network of the metazoan C. elegans. S Li CM Armstrong N Bertin H Ge S Milstein M Boxem PO Vidalain JD Han A Chesneau T Hao, Science 2004 303 540 543 10.1126/science.1091403 14704431
16. A human protein-protein interaction network: a resource for annotating the proteome. U Stelzl U Worm M Lalowski C Haenig FH Brembeck H Goehler M Stroedicke M Zenkner A Schoenherr S Koeppen, Cell 2005 122 957 968 10.1016/j.cell.2005.08.029 16169070
17. Towards a proteome-scale map of the human protein-protein interaction network. JF Rual K Venkatesan T Hao T Hirozane-Kishikawa A Dricot N Li GF Berriz FD Gibbons M Dreze N Ayivi-Guedehoussou, Nature 2005 437 1173 1178 10.1038/nature04209 16189514
18. Emergence of scaling in random networks. AL Barabasi R Albert, Science 1999 286 509 512 10.1126/science.286.5439.509 10521342
19. Error and attack tolerance of complex networks. R Albert H Jeong AL Barabasi, Nature 2000 406 378 382 10.1038/35019019 10935628
20. Does selection mold molecular networks? A Wagner, Sci STKE 2003 2003 PE41 14519859
21. Collective dynamics of 'small-world' networks. DJ Watts SH Strogatz, Nature 1998 393 440 442 10.1038/30918 9623998
22. Lethality and centrality in protein networks. H Jeong SP Mason AL Barabasi ZN Oltvai, Nature 2001 411 41 42 10.1038/35075138 11333967
23. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. A Wagner, Mol Biol Evol 2001 18 1283 1292 11420367
24. Network motifs in the transcriptional regulation network of Escherichia coli. SS Shen-Orr R Milo S Mangan U Alon, Nat Genet 2002 31 64 68 10.1038/ng881 11967538
25. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. LV Zhang OD King SL Wong DS Goldberg AH Tong G Lesage B Andrews H Bussey C Boone FP Roth, J Biol 2005 4 6 15982408 10.1186/jbiol23
26. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. H Ge Z Liu GM Church M Vidal, Nat Genet 2001 29 482 486 10.1038/ng776 11694880
27. A Bayesian networks approach for predicting protein-protein interactions from genomic data. R Jansen H Yu D Greenbaum Y Kluger NJ Krogan S Chung A Emili M Snyder JF Greenblatt M Gerstein, Science 2003 302 449 453 10.1126/science. 1087361 14564010
28. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). OG Troyanskaya K Dolinski AB Owen RB Altman D Botstein, Proc Natl Acad Sci USA 2003 100 8348 8353 12826619 10.1073/pnas.0832373100
29. A probabilistic functional network of yeast genes. I Lee SV Date AT Adai EM Marcotte, Science 2004 306 1555 1558 10.1126/science.1099511 15567862
30. Combining biological networks to predict genetic interactions. SL Wong LV Zhang AH Tong Z Li DS Goldberg OD King G Lesage M Vidal B Andrews H Bussey, Proc Natl Acad Sci USA 2004 101 15682 15687 15496468 10.1073/pnas.0406614101
31. Conserved patterns of protein interaction in multiple species. R Sharan S Suthram RM Kelley T Kuhn S McCuine P Uetz T Sittler RM Karp T Ideker, Proc Natl Acad Sci USA 2005 102 1974 1979 15687504 10.1073/pnas.0409522102
32. Discovery of biological networks from diverse functional genomic data. CL Myers D Robson A Wible MA Hibbs C Chiriac CL Theesfeld K Dolinski OG Troyanskaya, Genome Biology 2005 6 R114 16420673 10.1186/gb-2005-6-13-r114
33. Comparative assessment of large-scale data sets of protein-protein interactions. C von Mering R Krause B Snel M Cornell SG Oliver S Fields P Bork, Nature 2002 417 399 403 10.1038/nature750 12000970
34. Analyzing yeast protein-protein interaction data obtained from different sources. GD Bader CW Hogue, Nat Biotechnol 2002 20 991 997 10.1038/nbt1002-991 12355115
35. Is there a bias in proteome research? R Mrowka A Patzak H Herzel, Genome Res 2001 11 1971 1973 10.1101/gr.206701 11731485
36. The Yeast Protein Database (YPD): a curated proteome database for Saccharomyces cerevisiae. PE Hodges WE Payne JI Garrels, Nucleic Acids Res 1998 26 68 72 9399803 10.1093/nar/26.1.68
37. MIPS: a database for genomes and protein sequences. HW Mewes D Frishman U Guldener G Mannhaupt K Mayer M Mokrejs B Morgenstern M Munsterkotter S Rudd B Weil, Nucleic Acids Res 2002 30 31 34 11752246 10.1093/nar/30.1.31
38. MINT: a Molecular INTeraction database. A Zanzoni L Montecchi-Palazzi M Quondam G Ausiello M Helmer-Citterich G Cesareni, FEBS Lett 2002 513 135 140 10.1016/S0014-5793(01)03293-8 11911893
39. IntAct: an open source molecular interaction database. H Hermjakob L Montecchi-Palazzi C Lewington S Mudali S Kerrien S Orchard M Vingron B Roechert P Roepstorff A Valencia, Nucleic Acids Res 2004 32 (Database issue) D452 D455 14681455 10.1093/nar/gkh052
40. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. I Xenarios L Salwinski XJ Duan P Higney SM Kim D Eisenberg, Nucleic Acids Res 2002 30 303 305 11752321 10.1093/nar/30.1.303
41. BIND: the Biomolecular Interaction Network Database. GD Bader D Betel CW Hogue, Nucleic Acids Res 2003 31 248 250 12519993 10.1093/nar/gkg056
42. Development of human protein reference database as an initial platform for approaching systems biology in humans. S Peri JD Navarro R Amanchy TZ Kristiansen CK Jonnalagadda V Surendranath V Niranjan B Muthusamy TK Gandhi M Gronborg, Genome Res 2003 13 2363 2371 14525934 10.1101/gr.1680803
43. BioGRID: a general repository for interaction datasets. C Stark BJ Breitkreutz T Reguly L Boucher A Breitkreutz M Tyers, Nucleic Acids Res 2006 34 (Database issue) D535 D539 16381927 10.1093/nar/gkj109
44. BioGRID. http://www.thebiogrid.org
45. International Molecular Exchange Consortium. http://imex.sourceforge.net
46. The HUPO PSI's molecular interaction format: a community standard for the representation of protein interaction data. H Hermjakob L Montecchi-Palazzi G Bader J Wojcik L Salwinski A Ceol S Moore S Orchard U Sarkans C von Mering, Nat Biotechnol 2004 22 177 183 10.1038/nbt926 14755292
47. The Gene Ontology (GO) database and informatics resource. MA Harris J Clark A Ireland J Lomax M Ashburner R Foulger K Eilbeck S Lewis B Marshall C Mungall, Nucleic Acids Res 2004 32 (Database issue) D258 261 14681407
48. Ontological visualization of protein-protein interactions. HJ Drabkin C Hollenbeck DP Hill JA Blake, BMC Bioinformatics 2005 6 29 15707487 10.1186/1471-2105-6-29
49. Text-mining and information-retrieval services for molecular biology. M Krallinger A Valencia, Genome Biol 2005 6 224 15998455 10.1186/gb-2005-6-7-224
50. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. KR Christie S Weng R Balakrishnan MC Costanzo K Dolinski SS Dwight SR Engel B Feierbach DG Fisk JE Hirschman, Nucleic Acids Res 2004 32 (Database issue) D311 D314 14681421 10.1093/nar/gkh033
51. Saccharomyces Genome Database. http://www.yeastgenome.org
52. Sequencing and comparison of yeast species to identify genes and regulatory elements. M Kellis N Patterson M Endrizzi B Birren ES Lander, Nature 2003 423 241 254 10.1038/nature01644 12748633
53. The GRID: the General Repository for Interaction Datasets. BJ Breitkreutz C Stark M Tyers, Genome Biol 2003 4 R23 12620108 10.1186/gb-2003-4-3-r23
54. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. JD Han N Bertin T Hao DS Goldberg GF Berriz LV Zhang D Dupuy AJ Walhout ME Cusick FP Roth M Vidal, Nature 2004 430 88 93 10.1038/nature02555 15190252
55. Life cycles of successful genes. R Hoffmann A Valencia, Trends Genet 2003 19 79 81 10.1016/S0168-9525(02)00014-8 12547515
56. The COG database: an updated version includes eukaryotes. RL Tatusov ND Fedorova JD Jackson AR Jacobs B Kiryutin EV Koonin DM Krylov R Mazumder SL Mekhedov AN Nikolskaya, BMC Bioinformatics 2003 4 41 12969510 10.1186/1471-2105-4-41
57. Schizosaccharomyces pombe essential genes: a pilot study. A Decottignies I Sanchez-Perez P Nurse, Genome Res 2003 13 399 406 12618370 10.1101/gr.636103
58. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. EV Koonin ND Fedorova JD Jackson AR Jacobs DM Krylov KS Makarova R Mazumder SL Mekhedov AN Nikolskaya BS Rao, Genome Biol 2004 5 R7 14759257 10.1186/gb-2004-5-2-r7
59. On the number of protein-protein interactions in the yeast proteome. A Grigoriev, Nucleic Acids Res 2003 31 4157 4161 12853633 10.1093/nar/gkg466
60. The synthetic genetic interaction spectrum of essential genes. AP Davierwala J Haynes Z Li RL Brost MD Robinson L Yu S Mnaimneh H Ding H Zhu Y Chen, Nat Genet 2005 37 1147 1152 10.1038/ng1640 16155567
61. Some protein interaction data do not exhibit power law statistics. R Tanaka TM Yi J Doyle, FEBS Lett 2005 579 5140 5144 10.1016/j.febslet.2005.08.024 16143331
62. An exponential core in the heart of the yeast protein interaction network. JB Pereira-Leal B Audit JM Peregrin-Alvarez CA Ouzounis, Mol Biol Evol 2005 22 421 425 10.1093/molbev/msi024 15496552
63. Specificity and stability in topology of protein networks. S Maslov K Sneppen, Science 2002 296 910 913 10.1126/science.1065103 11988575
64. Systematic interpretation of genetic interactions using protein networks. R Kelley T Ideker, Nat Biotechnol 2005 23 561 566 10.1038/nbt1096 15877074
65. Osprey: a network visualization system. BJ Breitkreutz C Stark M Tyers, Genome Biol 2003 4 R22 12620107 10.1186/gb-2003-4-3-r22
66. Global architecture of genetic interactions on the protein network. O Ozier N Amin T Ideker, Nat Biotechnol 2003 21 490 491 10.1038/nbt0503-490 12721566
67. Global analysis of protein expression in yeast. S Ghaemmaghami WK Huh K Bower RW Howson A Belle N Dephoure EK O'Shea JS Weissman, Nature 2003 425 737 741 10.1038/nature02046 14562106
68. Global analysis of protein localization in budding yeast. WK Huh JV Falvo LC Gerke AS Carroll RW Howson JS Weissman EK O'Shea, Nature 2003 425 686 691 10.1038/nature02026 14562095
69. Stochastic model of protein-protein interaction: why signaling proteins need to be colocalized. NN Batada LA Shepp DO Siegmund, Proc Natl Acad Sci USA 2004 101 6445 6449 15096590 10.1073/pnas.0401314101
70. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. T Ideker V Thorsson JA Ranish R Christmas J Buhler JK Eng R Bumgarner DR Goodlett R Aebersold L Hood, Science 2001 292 929 934 10.1126/science.292.5518.929 11340206
71. Functional discovery via a compendium of expression profiles. TR Hughes MJ Marton AR Jones CJ Roberts R Stoughton CD Armour HA Bennett E Coffey H Dai YD He, Cell 2000 102 109 126 10.1016/S0092-8674(00)00015-5 10929718
72. Transcriptional regulatory code of a eukaryotic genome. CT Harbison DB Gordon TI Lee NJ Rinaldi KD Macisaac TW Danford NM Hannett JB Tagne DB Reynolds J Yoo, Nature 2004 431 99 104 10.1038/nature02800 15343339
73. An automated method for finding molecular complexes in large protein interaction networks. GD Bader CW Hogue, BMC Bioinformatics 2003 4 2 12525261 10.1186/1471-2105-4-2
74. Modular organization of cellular networks. AW Rives T Galitski, Proc Natl Acad Sci USA 2003 100 1128 1133 12538875 10.1073/pnas.0237338100
75. Protein complexes and functional modules in molecular networks. V Spirin LA Mirny, Proc Natl Acad Sci USA 2003 100 12123 12128 14517352 10.1073/pnas.2032324100
76. Inparanoid: a comprehensive database of eukaryotic orthologs. KP O'Brien M Remm EL Sonnhammer, Nucleic Acids Res 2005 33 (Database issue) D476 D480 15608241 10.1093/nar/gki107
77. The FlyBase database of the Drosophila genome projects and community literature. FlyBase Consortium, Nucleic Acids Res 2003 31 172 175 12519974 10.1093/nar/gkg094
78. FTICR mass spectrometry for qualitative and quantitative bioanalyses. JS Page CD Masselon RD Smith, Curr Opin Biotechnol 2004 15 3 11 10.1016/j.copbio.2004.01.002 15102459
79. Increasing specificity in high-throughput yeast two-hybrid experiments. PO Vidalain M Boxem H Ge S Li M Vidal, Methods 2004 32 363 370 10.1016/j.ymeth.2003.10.001 15003598
80. Modeling interactome: scale-free or geometric? N Przulj DG Corneil I Jurisica, Bioinformatics 2004 20 3508 3515 10.1093/bioinformatics/btg415 15284103
81. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. IK Jordan IB Rogozin YI Wolf EV Koonin, Genome Res 2002 12 962 968 12045149 10.1101/gr.87702. Article published online before print in May 2002
82. Evolutionary rate in the protein interaction network. HB Fraser AE Hirsh LM Steinmetz C Scharfe MW Feldman, Science 2002 296 750 752 10.1126/science. 1068696 11976460
83. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. IK Jordan YI Wolf EV Koonin, BMC Evol Biol 2003 3 1 12515583 10.1186/1471-2148-3-1
84. Hierarchical organization of modularity in metabolic networks. E Ravasz AL Somera DA Mongru ZN Oltvai AL Barabasi, Science 2002 297 1551 1555 10.1126/science.1073374 12202830
85. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. M Schuldiner SR Collins NJ Thompson V Denic A Bhamidipati T Punna J Ihmels B Andrews C Boone JF Greenblatt, Cell 2005 123 507 519 10.1016/j.cell.2005.08.031 16269340
86. Global analysis of protein phosphorylation in yeast. J Ptacek G Devgan G Michaud H Zhu X Zhu J Fasolo H Guo G Jona A Breitkreutz R Sopko, Nature 2005 438 679 684 10.1038/nature04187 16319894
87. The yeast cell-cycle network is robustly designed. F Li T Long Y Lu Q Ouyang C Tang, Proc Natl Acad Sci USA 2004 101 4781 4786 15037758 10.1073/pnas.0305937101
88. Formation of regulatory patterns during signal propagation in a mammalian cellular network. A Ma'ayan SL Jenkins S Neves A Hasseldine E Grace B Dubin-Thaler NJ Eungdamrong G Weng PT Ram JJ Rice, Science 2005 309 1078 1083 10.1126/science.1108876 16099987
89. Reactome: a knowledgebase of biological pathways. G Joshi-Tope M Gillespie I Vastrik P D'Eustachio E Schmidt B de Bono B Jassal GR Gopinath GR Wu L Matthews, Nucleic Acids Res 2005 33 (Database issue) D428 D432 15608231 10.1093/nar/gki072
90. KEGG: Kyoto Encyclopedia of Genes and Genomes. M Kanehisa S Goto, Nucleic Acids Res 2000 28 27 30 10592173 10.1093/nar/28.1.27
91. Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. AK Ramani RC Bunescu RJ Mooney EM Marcotte, Genome Biol 2005 6 R40 15892868 10.1186/gb-2005-6-5-r40
92. A new approach to decoding life: systems biology. T Ideker T Galitski L Hood, Annu Rev Genomics Hum Genet 2001 2 343 372 10.1146/annurev.genom.2.1.343 11701654
93. Textpresso: an ontology-based information retrieval and extraction system for biological literature. HM Muller EE Kenny PW Sternberg, PLoS Biol 2004 2 e309 15383839 10.1371/journal.pbio.0020309
94. Cluster analysis and display of genome-wide expression patterns. MB Eisen PT Spellman PO Brown D Botstein, Proc Natl Acad Sci USA 1998 95 14863 14868 9843981 10.1073/pnas.95.25.14863
95. Gaining confidence in high-throughput protein interaction networks. JS Bader A Chaudhuri JM Rothberg J Chant, Nat Biotechnol 2004 22 78 85 10.1038/nbt924 14704708
96. COG database. http://www.ncbi.nlm.nih.gov/COG
97. Cytoscape: a software environment for integrated models of biomolecular interaction networks. P Shannon A Markiel O Ozier NS Baliga JT Wang D Ramage N Amin B Schwikowski T Ideker, Genome Res 2003 13 2498 2504 14597658 10.1101/gr.1239303
98. PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. I Donaldson J Martin B de Bruijn C Wolting V Lay B Tuekam S Zhang B Baskin GD Bader K Michalickova, BMC Bioinformatics 2003 4 11 12689350 10.1186/1471-2105-4-11
99. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. G Zhu PT Spellman T Volpe PO Brown D Botstein TN Davis B Futcher, Nature 2000 406 90 94 10.1038/35021046 10894548
100. Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. H Yoshimoto K Saltsman AP Gasch HX Li N Ogawa D Botstein PO Brown MS Cyert, J Biol Chem 2002 277 31079 31088 10.1074/jbc.M202718200 12058033
101. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec 1p. AP Gasch M Huang S Metzner D Botstein SJ Elledge PO Brown, Mol Biol Cell 2001 12 2987 3003 11598186
102. Genomic expression programs in the response of yeast cells to environmental changes. AP Gasch PT Spellman CM Kao O Carmel-Harel MB Eisen G Storz D Botstein PO Brown, Mol Biol Cell 2000 11 4241 4257 11102521
103. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. PT Spellman G Sherlock MQ Zhang VR Iyer K Anders MB Eisen PO Brown D Botstein B Futcher, Mol Biol Cell 1998 9 3273 3297 9843569
104. The transcriptional program of sporulation in budding yeast. S Chu J DeRisi M Eisen J Mulholland D Botstein PO Brown I Herskowitz, Science 1998 282 699 705 10.1126/science.282.5389.699 9784122
105. Exploring the metabolic and genetic control of gene expression on a genomic scale. JL DeRisi VR Iyer PO Brown, Science 1997 278 680 686 10.1126/science.278.5338.680 9381177
106. Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. P Sudarsanam VR Iyer PO Brown F Winston, Proc Natl Acad Sci USA 2000 97 3364 3369 10725359 10.1073/pnas.050407197
107. Transcriptional remodeling in response to iron deprivation in Saccharomyces cerevisiae. M Shakoury-Elizeh J Tiedeman J Rashford T Ferea J Demeter E Garcia R Rolfes PO Brown D Botstein CC Philpott, Mol Biol Cell 2004 15 1233 1243 14668481 10.1091/mbc.E03-09-0642
108. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. N Ogawa J DeRisi PO Brown, Mol Biol Cell 2000 11 4309 4321 11102525
109. Proteome survey reveals modularity of the yeast cell machinery. AC Gavin P Aloy P Grandi R Krause M Boesche M Marzioch C Rau LJ Jensen S Bastuck B Dumpelfeld, Nature 2006 440 631 636 16429126
110. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. NJ Krogan G Cagney H Yu G Zhong X Guo A Ignatchenko J Li S Pu N Datta AP Tikuisis, Nature 2006 440 637 643 16554755