1887

Chapter 45 : Principles and Practice of DNA Microarray Technology

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $30.00

Preview this chapter:
Zoom in
Zoomout

Principles and Practice of DNA Microarray Technology, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817497/9781555812232_Chap45-1.gif /docserver/preview/fulltext/10.1128/9781555817497/9781555812232_Chap45-2.gif

Abstract:

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

Key Concept Ranking

DNA Synthesis
0.56405866
RNA Polymerase II
0.5106383
Acetyl Coenzyme A
0.4972797
0.56405866
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
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
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817497.chap45
1. Aebersold, R.,, and M. Mann. 2003. Mass spectrometry-based proteomics. Nature 422:198207.
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 100:38893894.
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. 21:150156.
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 2:351356.
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. 29:365371.
7. Causton, H. C.,, J. Quackenbush,, and A. Brazma. 2003. Microarray Gene Expression Data Analysis: a Beginner’s Guide, p. 4069. 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 12:323337.
9. Churchill, G. A. 2002. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 32(Suppl.):490495.
10. Clark, T. A.,, C. W. Sugnet,, and M. Ares, Jr. 2002. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296:907910.
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 278:680686.
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. 4:417437.
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 99:1614416149.
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. 14:10431051.
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: 1486314868.
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. 75:46724675.
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 12:29873003.
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 11:42414257.
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 418:387391.
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 1:323333.
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. 272:2166121664.
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 1:2232.
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.):481489.
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. 19:342347.
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 102:109126.
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. 25:333337.
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 292:929934.
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 2:345350.
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 409:533538.
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. 20:81578167.
33. Jelinsky, S. A.,, and L. D. Samson. 1999. Global response of Saccharomyces cerevisiae to an alkylating agent. Proc. Natl. Acad. Sci. USA 96:14861491.
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 96:1311813123.
35. Kohrer, K.,, and H. Domdey. 1991. Preparation of high molecular weight RNA. Methods Enzymol. 194:398405.
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. 21:916927.
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. 31:248254.
38. Larkin, J. E.,, B. C. Frank,, H. Gavras,, R. Sultana,, and J. Quackenbush. 2005. Independence and reproducibility across microarray platforms. Nat. Methods 2:337344.
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 298:799804.
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. 28:327334.
42. Lin, D.,, D. L. Tabb,, and J. R. Yates III. 2003. Large-scale protein identification using mass spectrometry. Biochim. Biophys. Acta 1646:110.
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. 14:16751680.
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 116:121137.
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. 31:34773482.
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. 4:12931301.
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 98:98539858.
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. 21:43474368.
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. 21:1625.
50. Patterson, S. D.,, and R. H. Aebersold. 2003. Proteomics: the first decade and beyond. Nat. Genet. 33(Suppl):311323.
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. 24:11401150.
52. Phizicky, E.,, P. I. H. Bastiaens,, H. Zhu,, M. Snyder,, and S. Fields. 2003. Protein analysis on a proteomic scale. Nature 422:208215.
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 122:517527.
54. Quackenbush, J. 2001. Computational analysis of microarray data. Nat. Rev. Genet. 2:418427.
55. Rajagopalan, D. 2003. A comparison of statistical methods for analysis of high density oligonucleotide array data. Bioinformatics 19:14691476.
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 290:23062309.
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 109:437446.
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. 37:120125.
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 270:467470.
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. 10:50775086.
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 2:191204.
63. Shannon, W.,, R. Culverhouse,, and J. Duncan. 2003. Analyzing microarray data using cluster analysis. Pharmacogenomics 4:4152.
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. 24:11511161.
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. 17:974978.
66. Stekel, D. 2003. Microarray Bioinformatics, p. 6272. Cambridge University Press, Cambridge, United Kingdom.
67. Stekel, D. 2003. Microarray Bioinformatics, p. 7399. 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. 31:56765684.
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. 29:25492557.
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 98:51165121.
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. 4:387393.
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 87:16631667.
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 99:58605865.
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 100:31073112.
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 21:351365.
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 294:23572360.
78. Yang, Y. H.,, and T. Speed. 2002. Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3:579588.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error