DNA microarray technology for target identification and validation

Clinical and Experimental Pharmacology and Physiology

Volumn 33, Issue 5-6, 2006, Pages 496-503

  Jayapal, Manikandan ^a   Melendez, Alirio J ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Diagnostic; Disease; Drug discovery; Drug targets; Gene expression; Gene therapy; Genes; Microarrays; Validation

Indexed keywords

CELL CULTURE; CELL CYCLE; DATA ANALYSIS; DATA BASE; DNA MICROARRAY; DRUG RESPONSE; DRUG TARGETING; EXPERIMENTAL DESIGN; GENE IDENTIFICATION; GENE SEQUENCE; GENE TECHNOLOGY; GENE THERAPY; GENETIC DISORDER; GENOTYPE; HUMAN; IN VIVO STUDY; METHODOLOGY; PREDICTION; PROTEIN MICROARRAY; REGULATOR GENE; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; TISSUE MICROARRAY; VALIDATION PROCESS;

ANIMALS; CELLS, CULTURED; COLORECTAL NEOPLASMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOTYPE; HUMANS; MICE; MICE, TRANSGENIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; RNA INTERFERENCE; RNA, MESSENGER;

EID: 33745204684     PISSN: 03051870     EISSN: 14401681     Source Type: Journal    
DOI: 10.1111/j.1440-1681.2006.04398.x     Document Type: Review

References (82)

1. Venter JC, Adams MD, Myers EW et al. The sequence of the human genome. Science 2001 291 : 1304 51.
2. Lander ES, Linton LM, Birren B et al. Initial sequencing and analysis of the human genome. Nature 2001 409 : 860 921.
3. Chen Y, Dougherty ER, Bittner ML. Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Opt. 1997 2 : 364 74.
4. Eisen MB, Brown PO. DNA arrays for analysis of gene expression. Methods Enzymol. 1999 303 : 179 205.
5. Wang T, Hopkins D, Schmidt C et al. Identification of genes differentially over-expressed in lung squamous cell carcinoma using combination of cDNA subtraction and microarray analysis. Oncogene 2000 9 : 1519 28.
6. Schena M, Shalon D, Davis R, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995 270 : 467 70.
7. Debouck C, Goodfellow PN. DNA microarrays in drug discovery and development. Nat. Genet. 1999 21 : 48 50.
8. Chuaqui RF, Bonner RF, Best CJ et al. The genetics of cancer: A 3D model. Nat. Genet. 1999 21 : 38 41.
9. Gerhold DL, Jensen RV, Gullans SR. Better therapeutics through microarrays. Nat. Genet. 2002 32 : 547 51.
10. Heller RA, Schena M, Chai A et al. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc. Natl Acad. Sci. USA 1997 94 : 2150 5.
11. McCaffrey TA, Fu C, Du B et al. High-level expression of Egr-1 and Egr-1-inducible genes in mouse and human atherosclerosis. J. Clin. Invest. 2000 105 : 653 62.
12. Perou CM, Jeffrey SS, van de Rijn M et al. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. Proc. Natl Acad. Sci. USA 1999 96 : 9212 17.
13. Perou CM, Sorlie T, Eisen MB et al. Molecular portraits of breast tumours. Nature 2000 406 : 747 52.
14. Alon U, Barkai N, Notterman DA et al. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl Acad. Sci. USA 1999 96 : 6745 50.
15. Kaminski N, Allard JD, Pittet JF et al. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis. Proc. Natl Acad. Sci. USA 2000 97 : 1778 83.
16. Kennedy GC, Matsuzaki H, Dong S et al. Large-scale genotyping of complex DNA. Nat. Biotechnol. 2003 21 : 1233 7.
17. Ulger C, Toruner GA, Alkan M et al. Comprehensive genome-wide comparison of DNA and RNA level scan using microarray technology for identification of candidate cancer-related genes in the HL-60 cell line. Cancer Genet. Cytogenet. 2003 147 : 28 35.
18. MacBeath G. Protein microarrays and proteomics. Nat. Genet. 2002 32 : 526 32.
19. Braunschweig T, Chung JY, Hewitt SM. Tissue microarrays: Bridging the gap between research and the clinic. Expert Rev. Proteomics 2005 2 : 325 36.
20. Schena M, Davis RW. Genes, genome, and chips. In : Schena M (ed.). DNA Microarrays: A Practical Approach. Oxford University Press, New York. 2002 1 16.
21. Matsuzaki H, Loi H, Dong S et al. Parallel genotyping of over 10 0 00 SNPs using a oneprimer assay on a high-density oligonucleotide array. Genome Res. 2004 14 : 414 25.
22. Sellick GS, Garrett C, Houlston RS. A novel gene for neonatal diabetes maps to chromosome 10p12.1-p13. Diabetes 2003 52 : 2636 8.
23. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 1998 95 : 14 63 8.
24. Brazma A, Vilo J. Gene expression data analysis. Microbes Infect. 2001 3 : 823 9.
25. D'haeseleer P, Liang S, Somogyi R. Genetic network inference: From co-expression clustering to reverse engineering. Bioinformatics 2000 16 : 707 26.
26. Reghunathan R, Jayapal M, Hsu LY et al. Expression profile of immune response genes in patients with severe acute respiratory syndrome. BMC Immunol. 2005 6 : 1 11.
27. Toronen P, Kolehmainen M, Wong G, Castren E. Analysis of gene expression data using self-organizing maps. FEBS Lett. 1999 451 : 142 6.
28. Tamayo P, Slonim D, Mesirov J et al. Interpreting patterns of gene expression with selforganizing maps: Methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA 1999 96 : 2907 12.
29. Khan J, Wei JS, Ringner M, Saal LH et al. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat. Med. 2001 7 : 673 9.
30. Alter O, Brown PO, Botstein D. Singular value decomposition for genomewide expression data processing and modeling. Proc. Natl Acad. Sci. USA 2000 97 : 10 01 6.
31. Raychaudhuri S, Stuart JM, Altman RB. Principal components analysis to summarize microarray experiments: Application to sporulation time series. Pac. Symp. Biocomput. 2000 1 : 455 66.
32. Chuaqui RF, Bonner RF, Best CJ et al. Post-analysis follow-up and validation of microarray experiments. Nat. Genet. 2002 32 : 509 14.
33. Hedlund E, Karsten SL, Kudo L et al. Identification of a Hoxd10-regulated transcriptional network and combinatorial interactions with Hoxa10 during spinal cord development. J. Neurosci. Res. 2004 75 : 307 19.
34. Bertucci F, Borie N, Ginestier C et al. Identification and validation of an ERBB2 gene expression signature in breast cancers. Oncogene 2004 23 : 2564 75.
35. Ball C, Brazma A, Causton H et al. Standards for microarray data: An open letter. Environ. Health Perspect. 2004 12 : 666 7.
36. Zou J, Young S, Zhu F et al. Microarray profile of differentially expressed genes in a monkey model of allergic asthma. Genome Biol. 2002 3 : research0020.1 0020. 13.
37. Lee JH, Kaminski N, Dolganov G et al. Interleukin-13 induces dramatically different transcriptional programs in three human airway cell types. Am. J. Respir. Cell. Mol. Biol. 2001 25 : 474 85.
38. Temple R, Allen E, Fordham J et al. Microarray analysis of eosinophils reveals a number of candidate survival and apoptosis genes. Am. J. Respir. Cell. Mol. Biol. 2001 25 : 425 33.
39. Zimmermann N, King NE, Laporte J et al. Dissection of experimental asthma with DNA microarray analysis identifies arginase in asthma pathogenesis. J. Clin. Invest. 2003 111 : 1863 74.
40. Cherkasova E, Laassri M, Chizhikov V et al. Microarray analysis of evolution of RNA viruses: Evidence of circulation of virulent highly divergent vaccine-derived polioviruses. Proc. Natl Acad. Sci. USA 2003 100 : 9398 403.
41. Manna D, Breier AM, Higgins NP. Microarray analysis of transposition targets in Escherichia coli: The impact of transcription. Proc. Natl Acad. Sci. USA 2004 101 : 9780 5.
42. Okamoto T, Suzuki T, Yamamoto N. Microarray fabrication with covalent attachment of DNA using bubble jet technology. Nat. Biotechnol. 2000 18 : 438 41.
43. Rioja I, Clayton CL, Graham SJ, Life PF, Dickson MC. Gene expression profiles in the rat streptococcal cell wall-induced arthritis model identified using microarray analysis. Arthritis Res. Ther. 2005 7 : 101 17.
44. Baechler EC, Batliwalla FM, Karypis G et al. Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc. Natl Acad. Sci. USA 2003 100 : 2610 15.
45. Hakonarson H, Halapi E, Whelan R, Gulcher J, Stefansson K, Grunstein MM. Association between IL-1beta/TNF-alpha-induced glucocorticoid-sensitive changes in multiple gene expression and altered responsiveness in airway smooth muscle. Am. J. Respir. Cell. Mol. Biol. 2001 25 : 761 71.
46. Petty TL. COPD in perspective. Chest 2002 121 : 116 20.
47. Yamanaka Y, Tamari M, Nakahata T, Nakamura Y. Gene expression profiles of human small airway epithelial cells treated with low doses of 14- and 16-membered macrolides. Biochem. Biophys. Res. Commun. 2001 287 : 198 203.
48. Schaner ME, Ross DT, Ciaravino G et al. Gene expression patterns in ovarian carcinomas. Mol. Biol. Cell 2003 14 : 4376 86.
49. Ramaswamy S, Tamayo P, Rifkin R et al. Multiclass cancer diagnosis using tumor gene expression signatures. Proc. Natl Acad. Sci. USA 2001 98 : 15 49 54.
50. West M, Blanchette C, Dressman H et al. Predicting the clinical status of human breast cancer by using gene expression profiles. Proc. Natl Acad. Sci. USA 2001 98 : 11 62 7.
51. Hideshima T, Mitsiades C, Akiyama M et al. Molecular mechanisms mediating antimyeloma activity of proteasome inhibitor PS-341. Blood 2003 101 : 1530 4.
52. Koehler A, Bataille F, Schmid C et al. Gene expression profiling of colorectal cancer and metastases divides tumours according to their clinicopathological stage. J. Pathol. 2004 204 : 65 74.
53. Scherf U, Ross DT, Waltham M et al. A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 2000 24 : 236 44.
54. Velasco AM, Gillis KA, Li Y et al. Identification and validation of novel androgen-regulated genes in prostate cancer. Endocrinology 2004 145 : 3913 24.
55. DePrimo SE, Wong LM, Khatry DB et al. Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: A novel strategy for biomarker identification. BMC Cancer 2003 3 : 3.
56. Golub TR, Slonim DK, Tamayo P et al. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 1999 286 : 531 7.
57. Ross DT, Scherf U, Eisen MB et al. Systematic variation in gene expression patterns in human cancer cell lines. Nat. Genet. 2000 24 : 227 35.
58. Nishigaki M, Aoyagi K, Danjoh I et al. Discovery of aberrant expression of R.-RAS by cancer-linked DNA hypomethylation in gastric cancer using microarrays. Cancer Res. 2005 65 : 2115 24.
59. Zhang HG, Hyde K, Page GP et al. Novel tumor necrosis factor alpha-regulated genes in rheumatoid arthritis. Arthritis Rheum. 2004 50 : 420 31.
60. Poulsen CB, Penkowa M, Borup R et al. Brain response to traumatic brain injury in wild-type and interleukin-6 knockout mice: A microarray analysis. J. Neurochem. 2005 92 : 417 32.
61. Chattopadhyay S, Kingsley E, Serour A, Curran TM, Brooks AI, Pearce DA. Altered gene expression in the eye of a mouse model for batten disease. Invest. Ophthalmol. Vis. Sci. 2004 45 : 2893 905.
62. Iglesias A, Murga M, Laresgoiti U et al. Diabetes and exocrine pancreatic insufficiency in E2F1/E2F2 double-mutant mice. J. Clin. Invest. 2004 113 : 1398 407.
63. Yamashita DS, Dodds RA. Cathepsin K and the design of inhibitors of cathepsin K. Curr. Pharm. Des. 2000 6 : 1 24.
64. Saftig P, Hunziker E, Wehmeyer O et al. Impaired osteoclastic bone resorption leads to osteopetrosis in cathepsin-K-deficient mice. Proc. Natl Acad. Sci. USA. 1998 95 : 13 53 8.
65. Verma UN, Surabhi RM, Schmaltieg A, Becerra C, Gaynor RB. Small interfering RNAs directed against beta-catenin inhibit the in vitro and in vivo growth of colon cancer cells. Clin. Cancer Res. 2003 9 : 1291 300.
66. Yang G, Thompson JA, Fang B, Liu J. Silencing of H-ras gene expression by retrovirus-mediated siRNA decreases transformation efficiency and tumorgrowth in a model of human ovarian cancer. Oncogene 2003 22 : 5694 701.
67. Chesler EJ, Lu L, Shou S et al. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat. Genet. 2005 37 : 233 42.
68. Haines JL, Hauser MA, Schmidt S et al. Complement factor H variant increases the risk of age-related macular degeneration. Science 2005 308 : 362 4.
69. Koed K, Wiuf C, Christensen LL et al. High-density single nucleotide polymorphism array defines novel stage and location-dependent allelic imbalances in human bladder tumors. Cancer Res. 2005 65 : 34 45.
70. Klein RJ, Zeiss C, Chew EY et al. Complement factor H polymorphism in age-related macular degeneration. Science 2005 308 : 385 9.
71. Pennacchio LA, Olivier M, Hubacek JA et al. An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing. Science 2001 294 : 169 73.
72. Stears RL, Martinsky T, Schena M. Trends in microarray analysis. Nat. Med. 2003 9 : 140 5.
73. White J. The future of microarray readers. Pharm. Discov. 2004 October : 30 4.
74. Wheeler DB, Bailey SN, Guertin DA, Carpenter AE, Higgins CO, Sabatini DM. RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells. Nat. Methods 2004 1 : 127 32.
75. Opalinska JB, Gewirtz AM. Nucleic-acid therapeutics: Basic principles and recent applications. Nat. Rev. Drug Discov. 2002 1 : 503 14.
76. Kurreck J. Antisense technologies. Improvement through novel chemical modifications. Eur. J. Biochem. 2003 270 : 1628 44.
77. Kononen J, Bubendorf L, Kallioniemi A et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med. 1998 4 : 844 7.
78. Moch H, Kononen J, Kallioniemi OP et al. Tissue microarray: What will they bring to molecular and anatomic pathology? Adv. Anat. Pathol. 2001 8 : 14 20.
79. Miller JC, Zhou H, Kwekel J et al. Antibody microarray profiling of human prostate cancer sera: Antibody screening and identification of potential biomarkers. Proteomics 2003 3 : 56 63.
80. Meldrum D. Automation for genomics, part two: Sequencers, microarrays, and future trends. Genome Res. 2000 10 : 1288 303.
81. Evans WE, Johnson JA. Pharmacogenomics: The inherited basis for interindividual differences in drug response. Annu. Rev. Genomics Hum. Genet. 2001 2 : 9 39.
82. D'Ambrosio C, Gatta L, Bonini S. The future of microarray technology: Networking the genome search. Allergy 2005 60 : 1219 26.