Application of Microarray Technology in Environmental and Comparative Physiology

Annual Review of Physiology

Volumn 65, Issue , 2003, Pages 231-259

  Gracey, Andrew Y ^a,b   Cossins, Andrew R ^a  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Acclimation; Adaptation; Evolution; Expression; Stress

Indexed keywords

ADAPTATION; CORRELATION ANALYSIS; DNA MICROARRAY; EVOLUTIONARY ADAPTATION; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOME; HUMAN; LIFESTYLE; MOLECULAR CLONING; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REGULATORY MECHANISM; REVIEW; SPECIES COMPARISON; ACCLIMATIZATION; ANIMAL; COMPARATIVE STUDY; ENVIRONMENT; GENETICS; METHODOLOGY; PHYSIOLOGY; SPECIES DIFFERENCE;

ACCLIMATIZATION; ANIMALS; ENVIRONMENT; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYSIOLOGY; SPECIES SPECIFICITY;

EID: 0037974525     PISSN: 00664278     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.physiol.65.092101.142716     Document Type: Review

References (150)

1. The C. elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: aplatform for investigating biology. Science 282:2012-18
2. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
3. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, et al. 2000. The genome sequence of Drosophila melanogaster. Science 287:2185-95
4. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, et al. 1996. Life with 6000 genes. Science 274:63-67
5. Krogh A. 1929. Progress of physiology. Am. J. Physiol. 90:243-51
6. Gygi SP, Rochon Y, Franza BR, Aebersold R. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19:1720-30
7. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, et al. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292:929-34
8. Brown PO, Botstein D. 1999. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21:33-37
9. Los DA, Murata N. 1998. Structure and expression of fatty-acid desaturases. Biochim. Biophys. Acta 1394:3-15
10. 9-desaturase by transcriptional and post-translational mechanisms. Science 271:815-18
11. 9-desaturase expression in the liver of carp (Cyprinus carpio L.). J. Exp. Biol. 203 (Pt. 3):641-50
12. Zatsepina OG, Velikodvorskaia VV, Molodtsov VB, Garbuz D, Lerman DN, et al. 2001. A Drosophila melanogaster strain from sub-equatorial Africa has exceptional thermotolerance but decreased Hsp70 expression. J. Exp. Biol. 204:1869-81
13. Wen X, Fuhrman S, Michaels GS, Carr DB, Smith S, et al. 1998. Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl. Acad. Sci. USA 95:334-39
14. DeRisi J, van den Hazel B, Marc P, Balzi E, Brown P, et al. 2000. Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants. FEBS Lett. 470:156-60
15. Chu S, Derisi J, Eisen M, Mulholland J, Botstein D, et al. 1998. The transcriptional program of sporulation in budding yeast. Science 282:699-705
16. Pandey A, Mann M. 2000. Proteomics to study genes and genomes. Nature 405:837-46
17. Golling G, Amsterdam A, Sun Z, Antonelli M, Maldonado E, et al. 2002. Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Nat. Genet. 31:135-40
18. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Lab. Press
19. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW. 1998. Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16:301-6
20. Shalon D, Smith SJ, Brown PO. 1996. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6:639-45
21. Hegde P, Qi R, Abernathy K, Gay C, Dharap S, et al. 2000. A concise guide to cDNA microarray analysis. Biotechniques 29:548-50, 52-54, 56
22. Eisen MB, Brown PO. 1999. DNA arrays for analysis of gene expression. Methods Enzymol. 303:179-205
23. Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G. 1999. Making and reading microarrays. Nat. Genet. 21:15-19
24. Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ. 2000. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 28:4552-57
25. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. 1999. High density synthetic oligonucleotide arrays. Nat. Genet. 21:20-24
26. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, et al. 2001. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19:342-47
27. Clark TA, Sugnet CW, Ares M Jr. 2002. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296:907-10
28. Hu GK, Madore SJ, Moldover B, Jatkoe T, Balaban D, et al. 2001. Predicting splice variant from DNA chip expression data. Genome Res. 11:1237-45
29. Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, et al. 2001. Experimental annotation of the human genome using microarray technology. Nature 409:922-27
30. Modrek B, Lee C. 2002. A genomic view of alternative splicing. Nat. Genet. 30:13-19
31. Iseli C, Stevenson BJ, de Souza SJ, Samaia HB, Camargo AA, et al. 2002. Long-range heterogeneity at the 3′ ends of human mRNAs. Genome Res. 12:1068-74
32. Boise LH, Gonzalez-Garcia M, Postema CE, Ding L, Lindsten T, et al. 1993. bcl-x, a bcl-2-related gene that functions as a dominant regulator of apoptotic cell death. Cell 74:597-608
33. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, et al. 2002. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30:e15
34. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G. 2001. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat. Genet. 29:389-95
35. Gardiner-Garden M, Littlejohn TG. 2001. A comparison of microarray databases. Brief. Bioinform. 2:143-58
36. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, et al. 2001. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat. Genet. 29:365-71
37. Novak JP, Sladek R, Hudson TJ. 2002. Characterization of variability in largescale gene expression data: implications for study design. Genomics 79:104-13
38. Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, et al. 1999. The transcriptional program in the response of human fibroblasts to serum. Science 283:83-87
39. Misra J, Schmitt W, Hwang D, Hsiao LL, Gullans S, et al. 2002. Interactive exploration of microarray gene expression patterns in a reduced dimensional space. Genome Res. 7:1112-20
40. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, et al. 2000. Functional discovery via a compendium of expression profiles. Cell 102:109-26
41. Kerr MK, Martin M, Churchill GA. 2000. Analysis of variance for gene expression microarray data. J. Comput. Biol. 7:819-37
42. Kerr MK, Churchill GA. 2001. Experimental design for gene expression microarrays. Biostatistics 2:183-201
43. Raychaudhuri S, Sutphin PD, Chang JT, Altman RB. 2001. Basic microarray analysis: grouping and feature reduction. Trends Biotechnol. 19:189-93
44. Quackenbush J. 2001. Computational analysis of microarray data. Nat. Rev. Genet. 2:418-27
45. Sherlock G. 2000. Analysis of large-scale gene expression data. Curr. Opin. Immunol. 12:201-5
46. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, et al. 1999. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA 96:2907-12
47. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:14863-68
48. Bozinov D, Rahnenfuhrer J. 2002. Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering. Bioinformatics 18:747-56
49. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, et al. 1999. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286:531-37
50. Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, et al. 2000. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl. Acad. Sci. USA 97:262-67
51. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, et al. 2000. Molecular portraits of human breast tumours. Nature 406:747-52
52. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, et al. 2001. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc. Natl. Acad. Sci. USA 98:13790-95
53. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, et al. 2000. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403:503-11
54. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, et al. 2002. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415:436-42
55. van't Veer LJ, Dai HY, van de Vijver MJ, He YDD, Hart AAM, et al. 2002. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530-36
56. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, et al. 2001. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl. Acad. Sci. USA 98:10869-74
57. Kim SK, Lund J, Kiraly M, Duke K, Jiang M, et al. 2001. A gene expression map for Caenorhabditis elegans. Science 293:2087-92
58. Niehrs C, Pollet N. 1999. Synexpression groups in eukaryotes. Nature 402:483-87
59. Gracey AY, Troll JV, Somero GN. 2001. Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proc. Natl. Acad. Sci. USA 98:1993-98
60. Soares MB, Bonaldo MF, Jelene P, Su L, Lawton L, Efstratiadis A. 1994. Construction and characterization of a normalized cDNA library. Proc. Natl. Acad. Sci. USA 91:9228-32
61. Adams MD, Soares MB, Kerlavage AR, Fields C, Venter JC. 1993. Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library. Nat. Genet. 4:373-80
62. Huang X, Madan A. 1999. CAP3: a DNA sequence assembly program. Genome Res. 9:868-77
63. Carninci P, Shibata Y, Hayatsu N, Sugahara Y, Shibata K, et al. 2000. Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res. 10:1617-30
64. Sagerstrom CG, Sun BI, Sive HL. 1997. Subtractive cloning: past, present, and future. Annu. Rev. Biochem. 66:751-83
65. Bonaldo MDF, Lennon G, Soares MB. 1996. Normalization and subtraction: 2 approaches to facilitate gene discovery. Genome Res. 6:791-806
66. Loftus SK, Chen Y, Gooden G, Ryan JF, Birznieks G, et al. 1999. Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis. Proc. Natl. Acad. Sci. USA 96:9277-80
67. Whitfield CW, Band MR, Bonaldo MF, Kumar CG, Liu L, et al. 2002. Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee. Genome Res. 12:555-66
68. Oleksiak MF, Kolell KJ, Crawford DL. 2001. Utility of natural populations for microarray analyses: isolation of genes necessary for functional genomic studies. Mar. Biotechnol. 3:S203-S11
69. Meier-Ewert S, Maier E, Ahmadi A, Curtis J, Lehrach H. 1993. An automated approach to generating expressed sequence catalogues. Nature 361:375-76
70. Clark MD, Hennig S, Herwig R, Clifton SW, Marra MA, et al. 2001. An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library. Genome Res. 11: 1594-602
71. Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, et al. 1996. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93:6025-30
72. Rebrikov DV, Britanova OV, Gurskaya NG, Lukyanov KA, Tarabykin VS, Lukyanov SA. 2000. Mirror orientation selection (MOS): a method for eliminating false positive clones from libraries generated by suppresion subtraction hybridisation. Nucleic Acids Res. 28:E90
73. Yang GP, Ross DT, Kuang WW, Brown PO, Weigel RJ. 1999. Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. Nucleic Acids Res. 27:1517-23
74. Coimbra RS, Weil D, Brottier P, Blanchard S, Levi M, et al. 2002. A subtracted cDNA library from the zebrafish (Danio rerio) embryonic inner ear. Genome Res. 12:1007-11
75. Keselman HJ, Cribbie R, Holland B. 2002. Controlling the rate of Type I error over a large set of statistical tests. Br. J. Math. Stat. Psychol. 55 (Pt. 1):27-39
76. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57:289-300
77. Ideker T, Thorsson V, Siegel AF, Hood LE. 2000. Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data. J. Comput. Biol. 7:805-17
78. Pritchard CC, Hsu L, Delrow J, Nelson PS. 2001. Project normal: defining normal variance in mouse gene expression. Proc. Natl. Acad. Sci. USA 98:13266-71
79. Huang Q, Liu D, Majewski P, Schulte LC, Korn JM, et al. 2001. The plasticity of dendritic cell responses to pathogens and their components. Science 294:870-75
80. Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, et al. 2002. Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc. Natl. Acad. Sci. USA 99:972-77
81. Storch KF, Lipan O, Leykin I, Viswanathan N, Davis FC, et al. 2002. Extensive and divergent circadian gene expression in liver and heart. Nature 417:78-83
82. Kita Y, Shiozawa N, Jin WH, Majewski RR, Besharse JC, et al. 2002. Implications of circadian gene expression in kidney, liver and the effects of fasting on pharmacogenomic studies. Pharmacogenetics 12:55-65
83. Cao SX, Dhahbi JM, Mote PL, Spindler SR. 2001. Genomic profiling of short-and long-term caloric restriction effects in the liver of aging mice. Proc. Natl. Acad. Sci. USA 98:10630-35
84. Burness GP, Leary SC, Hochachka PW, Moyes CD. 1999. Allometric scaling of RNA, DNA, and enzyme levels: an intraspecific study. Am. J. Physiol. Regulatory Integrative Comp. Physiol. 277:R1164-R70
85. Brem RB, Yvert G, Clinton R, Kruglyak L. 2002. Genetic dissection of transcriptional regulation in budding yeast Science 296:752-55
86. Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, et al. 2002. Intra-and interspecific variation in primate gene expression patterns. Science 296:340-43
87. Kato M, Seki N, Sugano S, Hashimoto K, Masuho Y, et al. 2001. Identification of sonic hedgehog-responsive genes using cDNA microarray. Biochem. Biophys. Res. Commun. 289:472-78
88. White KP. 2001. Functional genomics and the study of development, variation and evolution. Nat. Rev. Genet. 2:528-37
89. Aita VM, Christiane AM, Gilliam TC. 1999. Mapping complex traits in diseases of the hair and skin. Exp. Dermatol. 8:439-52
90. Gibson G. 2002. Microarrays in ecology and evolution: a preview. Mol. Ecol. 11:17-24
91. Bornholdt S. 2001. Modeling genetic networks and their evolution: a complex dynamical systems perspective. Biol. Chem. 382:1289-99
92. Doerge RW. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nat. Rev. Genet. 3:43-52
93. Eaves IA, Wicker LS, Ghandour G, Lyons PA, Peterson LB, et al. 2002. Combining mouse congenic strains and microarray gene expression analyses to study a complex trait: the NOD model of type 1 diabetes. Genome Res. 12:232-43
94. Kawamoto S, Ohnishi T, Kita H, Chisaka O, Okubo K. 1999. Expression profiling by iAFLP: a PCR-based method for genome-wide gene expression profiling. Genome Res. 9:1305-12
95. Gill RT, Wildt S, Yang YT, Ziesman S, Stephanopoulos G. 2002. Genome-wide screening for trait conferring genes using DNA microarrays. Proc. Natl. Acad. Sci. USA 99:7033-38
96. Ferea TL, Botstein D, Brown PO, Rosenzweig RF. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. USA 96:9721-26
97. Riehle MM, Bennett AF, Long AD. 2001. Genetic architecture of thermal adaptation in Escherichia coli. Proc. Natl. Acad. Sci. USA 98:525-30
98. Wagner A. 2000. Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate. Proc. Natl. Acad. Sci. USA 97:6579-84
99. Streelman JT, Kocher TD. 2000. From phenotype to genotype. Evol. Dev. 2:166-73
100. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11:4241-57
101. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, et al. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12:323-37
102. Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO. 2001. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Meclp. Mol. Biol. Cell 12:2987-3003
103. Nautiyal S, DeRisi JL, Blackburn EH. 2002. The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 99:9316-21
104. Carroll AS, Bishop AC, DeRisi JL, Shokat KM, O'Shea EK. 2001. Chemical inhibition of the Pho85 cyclin-dependent kinase reveals a role in the environmental stress response. Proc. Natl. Acad. Sci. USA 98:12578-83
105. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, et al. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-6
106. Deleted in proof
107. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-45
108. Cossins AR, Bowler K. 1987. The Temperature Biology of Animals. London: Chapman & Hall. 339 pp.
109. Somero GN, DeVries AL. 1967. Temperature tolerance of some Antarctic fishes. Science 156:257-58
110. Clark EA, Golub TR, Lander ES, Hynes RO. 2000. Genomic analysis of metastasis reveals an essential role for RhoC. Nature 406:532-35
111. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, et al. 2002. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. USA 99:4465-70
112. Raychaudhuri S, Chang JT, Sutphin PD, Altman RB. 2002. Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res. 12:203-14
113. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. 2000. Gene ontology: tool for the unification of biology. Nat. Genet. 25:25-29
114. The Gene Ontology Consortium. 2001. Creating the gene ontology resource: design and implementation. Genome Res. 11:1425-33
115. Khatri P, Draghici S, Ostermeier GC, Krawetz SA. 2002. Profiling gene expression using onto-express. Genomics 79:266-70
116. Relogio A, Schwager C, Richter A, Ansorge W, Valcarcel J. 2002. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res. 30:e51
117. Hacia JG, Edgemon K, Sun B, Stern D, Fodor SP, Collins FS. 1998. Two color hybridization analysis using high density oligonucleotide arrays and energy transfer dyes. Nucleic Acids Res. 26:3865-66
118. Frazer KA, Sheehan JB, Stokowski RP, Chen X, Hosseini R, et al. 2001. Evolutionarily conserved sequences on human chromosome 21. Genome Res. 11:1651-59
119. Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, et al. 2001. Comparative genomics of Listeria species. Science 294:849-52
120. Spiers AJ, Kahn SG, Bohannon J, Travisano M, Rainey PB. 2002. Adaptive divergence in experimental populations of Pseudomonas fluorescens. I. Genetic and phenotypic bases of Wrinkly Spreader fitness. Genetics 161:33-46
121. Jiang M, Ryu J, Kiraly M, Duke K, Reinke V, Kim SK. 2001. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 98:218-23
122. White KP, Rifkin SA, Hurban P, Hogness DS. 1999. Microarray analysis of Drosophila development during metamorphosis. Science 286:2179-84
123. Weiss MM, Hermsen MA, Meijer GA, van Grieken NC, Baak JP, et al. 1999. Comparative genomic hybridisation. Mol. Pathol. 52:243-51
124. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, et al. 1999. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 23:41-46
125. Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, et al. 2001. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet. 29:263-64
126. Cai WW, Mao JH, Chow CW, Damani S, Balmain A, Bradley A. 2002. Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays. Nat. Biotechnol. 20:393-96
127. Hodgson G, Hager JH, Volik S, Hariono S, Wernick M, et al. 2001. Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas. Nat. Genet. 29:459-64
128. Behr MA, Wilson MA, Gill WP, Salamon H, Schoolnik GK, et al. 1999. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284:1520-23
129. Murray AE, Lies D, Li G, Nealson K, Zhou J, Tiedje JM. 2001. DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc. Natl. Acad. Sci. USA 98:9853-58
130. Hughes TR, Roberts CJ, Dai HY, Jones AR, Meyer MR, et al. 2000. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat. Genet. 25:333-37
131. Clark J, Edwards S, John M, Rohr P, Gordon T, et al. 2002. Identification of amplified and expressed genes in breast cancer by comparative hybridization onto microarrays of randomly selected cDNA clones. Genes Chromosomes Cancer 34:104-14
132. Feder ME, Bennett AF, Burggren WW, Huey RB. 1987. New Directions in Ecological Physiology. Cambridge, UK: Cambridge Univ. Press
133. Amundson SA, Bittner M, Meltzer P, Trent J, Fornace AJ Jr. 2001. Induction of gene expression as a monitor of exposure to ionizing radiation. Radiat. Res. 156:657-61
134. Sesto A, Navarro M, Burslem F, Jorcano JL. 2002. Analysis of the ultraviolet B response in primary human keratinocytes using oligonucleotide microarrays. Proc. Natl. Acad. Sci. USA 99:2965-70
135. Cole J,Tsou R, Wallace K, Gibran N, Isik F. 2001. Early gene expression profile of human skin to injury using high-density cDNA microarrays. Wound Repair Regen. 9:360-70
136. Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, et al. 2002. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell 13:1977-2000
137. McCormick SM, Eskin SG, McIntire LV, Teng CL, Lu CM, et al. 2001. DNA microarray reveals changes in gene expression of shear stressed human umbilical vein endothelial cells. Proc. Natl. Acad. Sci. USA 98:8955-60
138. Blanchard RK, Moore JB, Green CL, Cousins RJ. 2001. Modulation of intestinal gene expression by dietary zinc status: effectiveness of cDNA arrays for expression profiling of a single nutrient deficiency. Proc. Natl. Acad. Sci. USA 98:13507-13
139. Gregoire FM, Zhang Q, Smith SJ, Tong C, Ross D, et al. 2002. Diet-induced obesity and hepatic gene expression alterations in C57BL/6J and ICAM-1-deficient mice. Am. J. Physiol. Endocrinol. Metab. 282:E703-E13
140. Lomax MI, Huang L, Cho YS, Gong TWL, Altschuler RA. 2000. Differential display and gene arrays to examine auditory plasticity. Hear. Res. 147:293-302
141. Andrews J, Bouffard GG, Cheadle C, Lu J, Becker KG, Oliver B. 2000. Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. Genome Res. 10:2030-43
142. Furlong EE, Andersen EC, Null B, White KP, Scott MP. 2001. Patterns of gene expression during Drosophila mesoderm development. Science 293:1629-33
143. Irving P, Troxler L, Heuer TS, Belvin M, Kopczynski C, et al. 2001. A genome-wide analysis of immune responses in Drosophila. Proc. Natl. Acad. Sci. USA 98:15119-24
144. De Gregorio E, Spellman PT, Rubin GM, Lemaitre B. 2001. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays. Proc. Natl. Acad. Sci. USA 98:12590-95
145. Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK. 2000. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium falciparum malaria. Mol. Microbiol. 35:6-14
146. Custodia N, Won SJ, Novillo A, Wieland M, Li C, Callard IP. 2001. Caenorhabditis elegans as an environmental monitor using DNA microarray analysis. Ann. NY Acad. Sci. 948:32-42
147. Guha Thakurta D, Palomar L, Stormo GD, Tedesco P, Johnson TE, et al. 2002. Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods. Genome Res. 12:701-12
148. Cavalieri D, Townsend JP, Hartl DL. 2000. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc. Natl. Acad. Sci. USA 97:12369-74
149. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO. 2002. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99:5860-65
150. Kanesaki Y, Suzuki I, Allakhverdiev SI, Mikami K, Murata N. 2002. Salt stress and hyperosmotic stress regulate the expression of different sets of genes in Synechocystis sp PCC 6803. Biochem. Biophys. Res. Commun. 290:339-48