Chapter 45 : Principles and Practice of DNA Microarray Technology

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This chapter describes the principles and detailed methodology for carrying out DNA microarray experiments using the yeast , and briefly reviews its attendant applications. Although microarray technology is widely used to study the transcriptome and its differential expression, this technology has also been applied in novel ways to study various aspects of cell biology. The two RNA samples, one derived from experimental RNA and the other from the control RNA sample, are converted to cDNA and labeled individually using fluorescent dyes such as cyanin 5 (Cy5) and cyanin 3 (Cy3). Next, the two labeled samples (targets) are combined in equal proportions and hybridized to a single microarray slide, therefore referred to as dual-color hybridization, involving competitive hybridization, i.e., simultaneous hybridization of the reference and experimental targets to a single microarray. The fluorescent signal emanating from each feature on the microarray slide is quantified by scanning the slide in a microarray scanner. The ratio of the fluorescence intensities emanating from the experimental versus control samples is then subjected to extensive statistical analyses to obtain the relative expression level of each gene on the microarray. A careful interpretation of the microarray data is important so that meaningful hypotheses can be generated for designing follow-up experiments. Further refinement of the statistical tools for microarray data analysis, including standardization of data normalization methods, would yield more robust and reliable data and enable comparison of microarray data generated in different laboratories and possibly find use in clinical practice.

Citation: Natarajan K, Marton M, Hinnebusch A. 2007. Principles and Practice of DNA Microarray Technology, p 978-994. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch45
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Overview of DNA microarray scheme.

Citation: Natarajan K, Marton M, Hinnebusch A. 2007. Principles and Practice of DNA Microarray Technology, p 978-994. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch45
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Image of FIGURE 2

Suggested workflow for comprehensive assessment of genome function. Integration of results from microarray studies into the results of proteome analysis, metabolome analysis, and protein-protein interaction data would provide a broad platform for assignment of genes to respective pathways and inference of the biological function of novel genes.

Citation: Natarajan K, Marton M, Hinnebusch A. 2007. Principles and Practice of DNA Microarray Technology, p 978-994. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch45
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1. Aebersold, R.,, and M. Mann. 2003. Mass spectrometry-based proteomics. Nature 422: 198 207.
2. Arava, Y.,, Y. Wang,, J. D. Storey,, C. Liu,, P. O. Brown,, and D. Herschlag. 2003. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100: 3889 3894.
3. Askenazi, M.,, E. M. Driggers,, D. A. Holtzman,, T. C. Norman,, S. Iverson,, D. P. Zimmer,, M. E. Boers,, P. R. Blomquist,, E. J. Martinez,, A. W. Monreal,, T. P. Feibelman,, M. E. Mayorga,, M. E. Maxon,, K. Sykes,, J. V. Tobin,, E. Cordero,, S. R. Salama,, J. Trueheart,, J. C. Royer,, and K. T. Madden. 2003. Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nat. Biotechnol. 21: 150 156.
4. Bammler, T.,, R. P. Beyer,, S. Bhattacharya,, G. A. Boorman,, A. Boyles,, B. U. Bradford,, R. E. Bumgarner,, P. R. Bushel,, K. Chaturvedi,, D. Choi,, M. L. Cunningham,, S. Deng,, H. K. Dressman,, R. D. Fannin,, F. M. Farin,, J. H. Freedman,, R. C. Fry,, A. Harper,, M. C. Humble,, P. Hurban,, T. J. Kavanagh,, W. K. Kaufmann,, K. F. Kerr,, L. Jing,, J. A. Lapidus,, M. R. Lasarev,, J. Li,, Y. J. Li,, E. K. Lobenhofer,, X. Lu,, R. L. Malek,, S. Milton,, S. R. Nagalla,, P. O’Malley J,, V. S. Palmer,, P. Pattee,, R. S. Paules,, C. M. Perou,, K. Phillips,, L. X. Qin,, Y. Qiu,, S. D. Quigley,, M. Rodland,, I. Rusyn,, L. D. Samson,, D. A. Schwartz,, Y. Shi,, J. L. Shin,, S. O. Sieber,, S. Slifer,, M. C. Speer,, P. S. Spencer,, D. I. Sproles,, J. A. Swenberg,, W. A. Suk,, R. C. Sullivan,, R. Tian,, R. W. Tennant,, S. A. Todd,, C. J. Tucker,, B. Van Houten,, B. K. Weis,, S. Xuan,, and H. Zarbl. 2005. Standardizing global gene expression analysis between laboratories and across platforms. Nat. Methods 2: 351 356.
5. Bowtell, D.,, and J. Sambrook. 2003. DNA Microarrays: a Molecular Cloning Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
6. Brazma, A.,, P. Hingamp,, J. Quackenbush,, G. Sherlock,, P. Spellman,, C. Stoeckert,, J. Aach,, W. Ansorge,, C. A. Ball,, H. C. Causton,, T. Gaasterland,, P. Glenisson,, F. C. Holstege,, I. F. Kim,, V. Markowitz,, J. C. Matese,, H. Parkinson,, A. Robinson,, U. Sarkans,, S. Schulze- Kremer,, J. Stewart,, R. Taylor,, J. Vilo,, and M. Vingron. 2001. Minimum Information About a Microarray Experiment (MIAME)—toward standards for microarray data. Nat. Genet. 29: 365 371.
7. Causton, H. C.,, J. Quackenbush,, and A. Brazma. 2003. Microarray Gene Expression Data Analysis: a Beginner’s Guide, p. 40 69. Blackwell Publishing Limited, Malden, MA.
8. Causton, H. C.,, B. Ren,, S. S. Koh,, C. T. Harbison,, E. Kanin,, E. G. Jennings,, T. I. Lee,, H. L. True,, E. S. Lander,, and R. A. Young. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12: 323 337.
9. Churchill, G. A. 2002. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 32(Suppl.): 490 495.
10. Clark, T. A.,, C. W. Sugnet,, and M. Ares, Jr. 2002. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296: 907 910.
11. Cui, X.,, and G. A. Churchill. 2003. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 4: 210.
12. DeRisi, J. L.,, V. R. Iyer,, and P. O. Brown. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680 686.
13. Dresen, I. M.,, J. Husing,, E. Kruse,, T. Boes,, and K. H. Jockel. 2003. Software packages for quantitative microarray- based gene expression analysis. Curr. Pharm. Biotechnol. 4: 417 437.
14. Dunham, M. J.,, H. Badrane,, T. Ferea,, J. Adams,, P. O. Brown,, F. Rosenzweig,, and D. Botstein. 2002. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 99: 16144 16149.
15. Edwards-Ingram, L. C.,, M. E. Gent,, D. C. Hoyle,, A. Hayes,, L. I. Stateva,, and S. G. Oliver. 2004. Comparative genomic hybridization provides new insights into the molecular taxonomy of the Saccharomyces sensu stricto complex. Genome Res. 14: 1043 1051.
16. Eisen, M. B.,, P. T. Spellman,, P. O. Brown,, and D. Botstein. 1998. Cluster analysis and display of genomewide expression patterns. Proc. Natl. Acad. Sci. USA 95: 14863 14868.
17. Fare, T. L.,, E. M. Coffey,, H. Dai,, Y. D. He,, D. A. Kessler,, K. A. Kilian,, J. E. Koch,, E. LeProust,, M. J. Marton,, M. R. Meyer,, R. B. Stoughton,, G. Y. Tokiwa,, and Y. Wang. 2003. Effects of atmospheric ozone on microarray data quality. Anal. Chem. 75: 4672 4675.
18. Gaillard, C.,, and F. Strauss. 1990. Ethanol precipitation of DNA with linear polyacrylamide as carrier. Nucleic Acids Res. 18: 378.
19. Gasch, A. P.,, M. Huang,, S. Metzner,, D. Botstein,, S. J. Elledge,, and P. O. Brown. 2001. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol. Biol. Cell 12: 2987 3003.
20. Gasch, A. P.,, P. T. Spellman,, C. M. Kao,, O. Carmel- Harel,, M. B. Eisen,, G. Storz,, D. Botstein,, and P. O. Brown. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11: 4241 4257.
21. Giaever, G.,, A. M. Chu,, L. Ni,, C. Connelly,, L. Riles,, S. Veronneau,, S. Dow,, A. Lucau-Danila,, K. Anderson,, B. Andre,, A. P. Arkin,, A. Astromoff,, M. El-Bakkoury,, R. Bangham,, R. Benito,, S. Brachat,, S. Campanaro,, M. Curtiss,, K. Davis,, A. Deutschbauer,, K. D. Entian,, P. Flaherty,, F. Foury,, D. J. Garfinkel,, M. Gerstein,, D. Gotte,, U. Guldener,, J. H. Hegemann,, S. Hempel,, Z. Herman,, D. F. Jaramillo,, D. E. Kelly,, S. L. Kelly,, P. Kotter,, D. LaBonte,, D. C. Lamb,, N. Lan,, H. Liang,, H. Liao,, L. Liu,, C. Luo,, M. Lussier,, R. Mao,, P. Menard,, S. L. Ooi,, J. L. Revuelta,, C. J. Roberts,, M. Rose,, P. Ross-Macdonald,, B. Scherens,, G. Schimmack,, B. Shafer,, D. D. Shoemaker,, S. Sookhai-Mahadeo,, R. K. Storms,, J. N. Strathern,, G. Valle,, M. Voet,, G. Volckaert,, C. Y. Wang,, T. R. Ward,, J. Wilhelmy,, E. A. Winzeler,, Y. Yang,, G. Yen,, E. Youngman,, K. Yu,, H. Bussey,, J. D. Boeke,, M. Snyder,, P. Philippsen,, R. W. Davis,, and M. Johnston. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387 391.
22. Griffin, T. J.,, S. P. Gygi,, T. Ideker,, B. Rist,, J. Eng,, L. Hood,, and R. Aebersold. 2002. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell. Proteomics 1: 323 333.
23. Hinnebusch, A. G. 1997. Translational regulation of yeast GCN4: a window on factors that control initiator-tRNA binding to the ribosome. J. Biol. Chem. 272: 21661 21664.
24. Hinnebusch, A. G.,, and K. Natarajan. 2002. Gcn4p, a master regulator of gene expression, is controlled at multiple levels by diverse signals of starvation and stress. Eukaryot. Cell 1: 22 32.
25. Holloway, A. J.,, R. K. van Laar,, R. W. Tothill,, and D. D. Bowtell. 2002. Options available—from start to finish— for obtaining data from DNA microarrays II. Nat. Genet. 32(Suppl.): 481 489.
26. Hughes, T. R.,, M. Mao,, A. R. Jones,, J. Burchard,, M. J. Marton,, K. W. Shannon,, S. M. Lefkowitz,, M. Ziman,, J. M. Schelter,, M. R. Meyer,, S. Kobayashi,, C. Davis,, H. Dai,, Y. D. He,, S. B. Stephaniants,, G. Cavet,, W. L. Walker,, A. West,, E. Coffey,, D. D. Shoemaker,, R. Stoughton,, A. P. Blanchard,, S. H. Friend,, and P. S. Linsley. 2001. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19: 342 347.
27. Hughes, T. R.,, M. J. Marton,, A. R. Jones,, C. J. Roberts,, R. Stoughton,, C. D. Armour,, H. A. Bennett,, E. Coffey,, H. Dai,, Y. D. He,, M. J. Kidd,, A. M. King,, M. R. Meyer,, D. Slade,, P. Y. Lum,, S. B. Stepaniants,, D. D. Shoemaker,, D. Gachotte,, K. Chakraburtty,, J. Simon,, M. Bard,, and S. H. Friend. 2000. Functional discovery via a compendium of expression profiles. Cell 102: 109 126.
28. Hughes, T. R.,, C. J. Roberts,, H. Dai,, A. R. Jones,, M. R. Meyer,, D. Slade,, J. Burchard,, S. Dow,, T. R. Ward,, M. J. Kidd,, S. H. Friend,, and M. J. Marton. 2000. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat. Genet. 25: 333 337.
29. Ideker, T.,, V. Thorsson,, J. A. Ranish,, R. Christmas,, J. Buhler,, J. K. Eng,, R. Bumgarner,, D. R. Goodlett,, R. Aebersold,, and L. Hood. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929 934.
30. Irizarry, R. A.,, D. Warren,, F. Spencer,, I. F. Kim,, S. Biswal,, B. C. Frank,, E. Gabrielson,, J. G. Garcia,, J. Geoghegan,, G. Germino,, C. Griffin,, S. C. Hilmer,, E. Hoffman,, A. E. Jedlicka,, E. Kawasaki,, F. Martinez- Murillo,, L. Morsberger,, H. Lee,, D. Petersen,, J. Quackenbush,, A. Scott,, M. Wilson,, Y. Yang,, S. Q. Ye,, and W. Yu. 2005. Multiple-laboratory comparison of microarray platforms. Nat. Methods 2: 345 350.
31. Iyer, V. R.,, C. E. Horak,, C. S. Scafe,, D. Botstein,, M. Snyder,, and P. O. Brown. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533 538.
32. Jelinsky, S. A.,, P. Estep,, G. M. Church,, and L. D. Samson. 2000. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol. Cell. Biol. 20: 8157 8167.
33. Jelinsky, S. A.,, and L. D. Samson. 1999. Global response of Saccharomyces cerevisiae to an alkylating agent. Proc. Natl. Acad. Sci. USA 96: 1486 1491.
34. Johannes, G.,, M. S. Carter,, M. B. Eisen,, P. O. Brown,, and P. Sarnow. 1999. Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc. Natl. Acad. Sci. USA 96: 13118 13123.
35. Kohrer, K.,, and H. Domdey. 1991. Preparation of high molecular weight RNA. Methods Enzymol. 194: 398 405.
36. Kuhn, K. M.,, J. L. DeRisi,, P. O. Brown,, and P. Sarnow. 2001. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell. Biol. 21: 916 927.
37. Kurdistani, S. K.,, D. Robyr,, S. Tavazoie,, and M. Grunstein. 2002. Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat. Genet. 31: 248 254.
38. Larkin, J. E.,, B. C. Frank,, H. Gavras,, R. Sultana,, and J. Quackenbush. 2005. Independence and reproducibility across microarray platforms. Nat. Methods 2: 337 344.
39. Lee, C.,, and M. Roy. 2004. Analysis of alternative splicing with microarrays: successes and challenges. Genome Biol. 5: 231.
40. Lee, T. I.,, N. J. Rinaldi,, F. Robert,, D. T. Odom,, Z. Bar- Joseph,, G. K. Gerber,, N. M. Hannett,, C. T. Harbison,, C. M. Thompson,, I. Simon,, J. Zeitlinger,, E. G. Jennings,, H. L. Murray,, D. B. Gordon,, B. Ren,, J. J. Wyrick,, J. B. Tagne,, T. L. Volkert,, E. Fraenkel,, D. K. Gifford,, and R. A. Young. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799 804.
41. Lieb, J. D.,, X. Liu,, D. Botstein,, and P. O. Brown. 2001. Promoter-specific binding of Rap1 revealed by genomewide maps of protein-DNA association. Nat. Genet. 28: 327 334.
42. Lin, D.,, D. L. Tabb,, and J. R. Yates III. 2003. Large-scale protein identification using mass spectrometry. Biochim. Biophys. Acta 1646: 1 10.
43. Lockhart, D. J.,, H. Dong,, M. C. Byrne,, M. T. Follettie,, M. V. Gallo,, M. S. Chee,, M. Mittmann,, C. Wang,, M. Kobayashi,, H. Horton,, and E. L. Brown. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14: 1675 1680.
44. Lum, P. Y.,, C. D. Armour,, S. B. Stepaniants,, G. Cavet,, M. K. Wolf,, J. S. Butler,, J. C. Hinshaw,, P. Garnier,, G. D. Prestwich,, A. Leonardson,, P. Garrett-Engele,, C. M. Rush,, M. Bard,, G. Schimmack,, J. W. Phillips,, C. J. Roberts,, and D. D. Shoemaker. 2004. Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 116: 121 137.
45. Luscombe, N. M.,, T. E. Royce,, P. Bertone,, N. Echols,, C. E. Horak,, J. T. Chang,, M. Snyder,, and M. Gerstein. 2003. Expressyourself: a modular platform for processing and visualizing microarray data. Nucleic Acids Res. 31: 3477 3482.
46. Marton, M. J.,, J. L. DeRisi,, H. A. Bennett,, V. Iyer,, M. R. Meyer,, C. J. Roberts,, R. Stoughton,, J. Burchard,, D. Slade,, H. Dai,, D. E. Bassett,, L. H. Haratwell,, P. O. Brown,, and S. H. Friend. 1998. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med. 4: 1293 1301.
47. Murray, A. E.,, D. Lies,, G. Li,, K. Nealson,, J. Zhou,, and J. M. Tiedje. 2001. DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc. Natl. Acad. Sci. USA 98: 9853 9858.
48. Natarajan, K.,, M. R. Meyer,, B. M. Jackson,, D. Slade,, C. J. Roberts,, A. G. Hinnebusch,, and M. J. Marton. 2001. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol. Cell. Biol. 21: 4347 4368.
49. Pascual-Ahuir, A.,, R. Serrano,, and M. Proft. 2001. The Sko1p repressor and Gcn4p activator antagonistically modulate stress-regulated transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 21: 16 25.
50. Patterson, S. D.,, and R. H. Aebersold. 2003. Proteomics: the first decade and beyond. Nat. Genet. 33(Suppl): 311 323.
51. Patterson, T. A.,, E. K. Lobenhofer,, S. B. Fulmer- Smentek,, P. J. Collins,, T. M. Chu,, W. Bao,, H. Fang,, E. S. Kawasaki,, J. Hager,, I. R. Tikhonova,, S. J. Walker,, L. Zhang,, P. Hurban,, F. de Longueville,, J. C. Fuscoe,, W. Tong,, L. Shi,, and R. D. Wolfinger. 2006. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat. Biotechnol. 24: 1140 1150.
52. Phizicky, E.,, P. I. H. Bastiaens,, H. Zhu,, M. Snyder,, and S. Fields. 2003. Protein analysis on a proteomic scale. Nature 422: 208 215.
53. Pokholok, D. K.,, C. T. Harbison,, S. Levine,, M. Cole,, N. M. Hannett,, T. I. Lee,, G. W. Bell,, K. Walker,, P. A. Rolfe,, E. Herbolsheimer,, J. Zeitlinger,, F. Lewitter,, D. K. Gifford,, and R. A. Young. 2005. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122: 517 527.
54. Quackenbush, J. 2001. Computational analysis of microarray data. Nat. Rev. Genet. 2: 418 427.
55. Rajagopalan, D. 2003. A comparison of statistical methods for analysis of high density oligonucleotide array data. Bioinformatics 19: 1469 1476.
56. Ren, B.,, F. Robert,, J. J. Wyrick,, O. Aparicio,, E. G. Jennings,, I. Simon,, J. Zeitlinger,, J. Schreiber,, N. Hannett,, E. Kanin,, T. L. Volkert,, C. J. Wilson,, S. P. Bell,, and R. A. Young. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306 2309.
57. Robyr, D.,, Y. Suka,, I. Xenarios,, S. K. Kurdistani,, A. Wang,, N. Suka,, and M. Grunstein. 2002. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109: 437 446.
58. Sambrook, J.,, and D. W. Russel. 2001. Molecular Cloning: a Laboratory Manual, 3rd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
59. Schadt, E. E.,, C. Li,, B. Ellis,, and W. H. Wong. 2001. Feature extraction and normalization algorithms for highdensity oligonucleotide gene expression array data. J. Cell. Biochem. Suppl. 37: 120 125.
60. Schena, M.,, D. Shalon,, R. W. Davis,, and P. O. Brown. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467 470.
61. Sellers, J. W.,, A. C. Vincent,, and K. Struhl. 1990. Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREBlike repressor that recognizes similar DNA sites. Mol. Cell. Biol. 10: 5077 5086.
62. Serikawa, K. A.,, X. L. Xu,, V. L. MacKay,, G. L. Law,, Q. Zong,, L. P. Zhao,, R. Bumgarner,, and D. R. Morris. 2003. The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae. Mol. Cell. Proteomics 2: 191 204.
63. Shannon, W.,, R. Culverhouse,, and J. Duncan. 2003. Analyzing microarray data using cluster analysis. Pharmacogenomics 4: 41 52.
64. Shi, L.,, L. H. Reid,, W. D. Jones,, R. Shippy,, J. A. Warrington,, S. C. Baker,, P. J. Collins,, F. de Longueville,, E. S. Kawasaki,, K. Y. Lee,, Y. Luo,, Y. A. Sun,, J. C. Willey,, R. A. Setterquist,, G. M. Fischer,, W. Tong,, Y. P. Dragan,, D. J. Dix,, F. W. Frueh,, F. M. Goodsaid,, D. Herman,, R. V. Jensen,, C. D. Johnson,, E. K. Lobenhofer,, R. K. Puri,, U. Schrf,, J. Thierry-Mieg,, C. Wang,, M. Wilson,, P. K. Wolber,, L. Zhang,, S. Amur,, W. Bao,, C. C. Barbacioru,, A. B. Lucas,, V. Bertholet,, C. Boysen,, B. Bromley,, D. Brown,, A. Brunner,, R. Canales,, X. M. Cao,, T. A. Cebula,, J. J. Chen,, J. Cheng,, T. M. Chu,, E. Chudin,, J. Corson,, J. C. Corton,, L. J. Croner,, C. Davies,, T. S. Davison,, G. Delenstarr,, X. Deng,, D. Dorris,, A. C. Eklund,, X. H. Fan,, H. Fang,, S. Fulmer-Smentek,, J. C. Fuscoe,, K. Gallagher,, W. Ge,, L. Guo,, X. Guo,, J. Hager,, P. K. Haje,, J. Han,, T. Han,, H. C. Harbottle,, S. C. Harris,, E. Hatchwell,, C. A. Hauser,, S. Hester,, H. Hong,, P. Hurban,, S. A. Jackson,, H. Ji,, C. R. Knight,, W. P. Kuo,, J. E. LeClerc,, S. Levy,, Q. Z. Li,, C. Liu,, Y. Liu,, M. J. Lombardi,, Y. Ma,, S. R. Magnuson,, B. Maqsodi,, T. McDaniel,, N. Mei,, O. Myklebost,, B. Ning,, N. Novoradovskaya,, M. S. Orr,, T. W. Osborn,, A. Papallo,, T. A. Patterson,, R. G. Perkins,, E. H. Peters,, R. Peterson, et al. 2006. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol. 24: 1151 1161.
65. Singh-Gasson, S.,, R. D. Green,, Y. Yue,, C. Nelson,, F. Blattner,, M. R. Sussman,, and F. Cerrina. 1999. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotechnol. 17: 974 978.
66. Stekel, D. 2003. Microarray Bioinformatics, p. 62 72. Cambridge University Press, Cambridge, United Kingdom.
67. Stekel, D. 2003. Microarray Bioinformatics, p. 73 99. Cambridge University Press, Cambridge, United Kingdom.
68. Tan, P. K.,, T. J. Downey,, E. L. Spitznagel, Jr.,, P. Xu,, D. Fu,, D. S. Dimitrov,, R. A. Lempicki,, B. M. Raaka,, and M. C. Cam. 2003. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 31: 5676 5684.
69. Tseng, G. C.,, M. K. Oh,, L. Rohlin,, J. C. Liao,, and W. H. Wong. 2001. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 29: 2549 2557.
70. Tusher, V. G.,, R. Tibshirani,, and G. Chu. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98: 5116 5121.
71. van de Peppel, J.,, P. Kemmeren,, H. van Bakel,, M. Radonjic,, D. van Leenen,, and F. C. P. Holstege. 2003. Monitoring global messenger RNA changes in externally controlled microarray experiments. EMBO Rep. 4: 387 393.
72. Van Gelder, R. N.,, M. E. von Zastrow,, A. Yool,, W. C. Dement,, J. D. Barchas,, and J. H. Eberwine. 1990. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc. Natl. Acad. Sci. USA 87: 1663 1667.
73. Wang, Y.,, C. L. Liu,, J. D. Storey,, R. J. Tibshirani,, D. Herschlag,, and P. O. Brown. 2002. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99: 5860 5865.
74. Washburn, M. P.,, A. Koller,, G. Oshiro,, R. R. Ulaszek,, D. Plouffe,, C. Deciu,, E. Winzeler,, and J. R. Yates III. 2003. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100: 3107 3112.
75. Watanabe, T.,, Y. Murata,, S. Oka,, and H. Iwahashi. 2004. A new approach to species determination for yeast strains: DNA microarray-based comparative genomic hybridization using a yeast DNA microarray with 6000 genes. Yeast 21: 351 365.
76. Wu, H.,, K. M. Kerr,, X. Cui,, and G. A. Churchill,. 2003. MAANOVA: a software package for the analysis of spotted cDNA microarray experiments. In G. Parmigiani,, E. S. Garett,, R. A. Irizarry,, and S. L. Zeger (ed.), The Analysis of Gene Expression Data: Methods and Software. Springer, New York, NY.
77. Wyrick, J. J.,, J. G. Aparicio,, T. Chen,, J. D. Barnett,, E. G. Jennings,, R. A. Young,, S. P. Bell,, and O. M. Aparicio. 2001. Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294: 2357 2360.
78. Yang, Y. H.,, and T. Speed. 2002. Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3: 579 588.

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