Technology Insight: Microarrays - Research and clinical applications

Nature Clinical Practice Endocrinology and Metabolism

Volumn 3, Issue 8, 2007, Pages 594-605

  Vlacich, Gregory ^a   Roe, Cheryl ^a   Webb, Gene C ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

Genome; Hormone; Microarray; Proteome; Transcriptome

Indexed keywords

ANDROGEN; ANTINEOPLASTIC AGENT; BIOLOGICAL MARKER; CARBOHYDRATE; DNA; LIPID; MESSENGER RNA; PROTEIN; RNA;

BREAST CANCER; CLUSTER ANALYSIS; DIABETES MELLITUS; DISEASE COURSE; ENDOCRINE TUMOR; GENE INTERACTION; GENE LOCUS; HUMAN; MICROARRAY ANALYSIS; NEUROFIBROMATOSIS; NORTHERN BLOTTING; PRIORITY JOURNAL; PROSTATE CANCER; QUALITY CONTROL; REVIEW; SIPPLE SYNDROME; SOUTHERN BLOTTING; TECHNOLOGY;

DIABETES MELLITUS; DNA; DNA, NEOPLASM; ENDOCRINE GLAND NEOPLASMS; HUMANS; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; PROTEOMICS; RNA, MESSENGER; TUMOR MARKERS, BIOLOGICAL;

EID: 34447628522     PISSN: 17458366     EISSN: 17458374     Source Type: Journal    
DOI: 10.1038/ncpendmet0580     Document Type: Review

References (66)

1. Southern EM (2000) Blotting at 25. Trends Biochem Sci 25: 585-588
2. Southern E et al. (1999) Molecular interactions on microarrays. Nat Genet 21 (suppl 1): S5-S9
3. Frei E et al. (1985) Cloning of the extra sex combs gene of Drosophila and its identification by P-element-mediated gene transfer. EMBO J 4: 979-987
4. DeLorenzi M et al. (1988) Evidence that the Abdominal-B r element function is conferred by a trans-regulatory homeoprotein. EMBO J 7: 3223-3231
5. Webb G et al. (1990) Location of gyrA on the physical map of the Escherichia coli chromosome. J Bacteriol 172: 6617
6. Brown DM (1993) A brief history of oligonucleotide synthesis. Methods Mol Biol 20: 1-17
7. Fodor SP et al. (1993) Multiplexed biochemical assays with biological chips. Nature 364: 555-556
8. NCBI GenBank Overview [http://www.ncbi.nlm.nih.gov/Genbank/] (accessed 24 April 2007)
9. Schena M et al. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 93: 10614-10619
10. White JC and Stryer L (1987) Photostability studies of phycobiliprotein fluorescent labels. Anal Biochem 161: 442-452
11. Ernst LA et al. (1989) Cyanine dye labeling reagents for sulfhydryl groups. Cytometry 10: 3-10
12. Minsky M (1988) Memoir on inventing the confocal scanning microscope. Scanning 10: 128-138
13. Norris AW and Kahn CR (2006) Analysis of gene expression in pathophysiological states: balancing false discovery and false negative rates. Proc Natl Acad Sci USA 103: 649-653
14. Kutlu B et al. (2004) New approaches for in silico identification of cytokine-modified β cell gene networks. Ann NY Acad Sci 1037: 41-58
15. Matsunaga T and Muramatsu MA (2005) Knowledge-based computational search for genes associated with the metabolic syndrome. Bioinformatics 21: 3146-3154
16. Dufva M and Christensen CB (2005) Diagnostic and analytical applications of protein microarrays. Expert Rev Proteomics 2: 41-48
17. LaBaer J and Ramachandran N (2005) Protein microarrays as tools for functional proteomics. Curr Opin Chem Biol 9: 14-19
18. Angeloni S et al. (2005) Glycoprofiling with microarrays of glycoconjugates and lectins. Glycobiology 15: 31-41
19. Kanter JL et al. (2006) Lipid microarrays identify key mediators of autoimmune brain inflammation. Nat Med 12: 138-143
20. Phizicky E et al. (2003) Protein analysis on a proteomic scale. Nature 422: 208-215
21. Bell J (2004) Predicting disease using genomics. Nature 429: 453-456
22. Lee TI and Young RA (2000) Transcription of eukaryotic protein-coding genes. Annu Rev Genet 34: 77-137
23. Lemon B and Tjian R (2000) Orchestrated response: a symphony of transcription factors for gene control. Genes Dev 14: 2551-2569
24. Emerson BM (2002) Specificity of gene regulation. Cell 109: 267-270
25. Matsuzaki H et al. (2004) Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods 1: 109-111
26. Bejjani BA et al. (2005) Array-based comparative genomic hybridization in clinical diagnosis. Expert Rev Mol Diagn 5: 421-429
27. van Steensel B and Henikoff S (2003) Epigenomic profiling using microarrays. Biotechniques 35: 346-357
28. Ragoussis J et al. (2006) Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research. PLoS Genet 2: e100
29. Wang SM (2007) Understanding SAGE data. Trends Genet 23: 42-50
30. Baggerman G et al. (2005) Gel-based versus gel-free proteomics: a review. Comb Chem High Throughput Screen 8: 669-677
31. Yuan M and Kendziorski C (2006) A unified approach for simultaneous gene clustering and differential expression identification. Biometrics 62: 1089-1098
32. Mocellin S and Rossi CR (2007) Principles of gene microarray data analysis. Adv Exp Med Biol 593: 19-30
33. Hanai T et al. (2006) Application of bioinformatics for DNA microarray data to bioscience, bioengineering and medical fields. J Biosci Bioeng 101: 377-384
34. Mount DW and Pandey R (2005) Using bioinformatics and genome analysis for new therapeutic interventions. Mol Cancer Ther 4: 1636-1643
35. Carella M et al. (2003) Nanotechnologies and microchips in genetic diseases. J Nephrol 16: 597-602
36. Boel E et al. (2000) Modulation of metabolism through transcriptional control has created new treatment opportunities for type 2 diabetes. Curr Pharm Biotechnol 1: 63-71
37. Nadler ST and Attie AD (2001) Please pass the chips: genomic insights into obesity and diabetes. J Nutr 131: 2078-2081
38. Perfetti R and D'Amico E (2003) The contribution of gene profile analysis to the design of a molecular approach to treat diabetes in humans. Diabetes Technol Ther 5: 421-423
39. Bell GI and Polonsky KS (2001) Diabetes mellitus and genetically programmed defects in β-cell function. Nature 414: 788-791
40. Odom DT et al. (2004) Control of pancreas and liver gene expression by HNF transcription factors. Science 303: 1378-1381
41. Song JY et al. (2005) Diagnosis of HNF-1α mutations on a PNA zip-code microarray by single base extension. Nucleic Acids Res 33: e19
42. Rasschaert J et al. (2003) Global profiling of double stranded RNA- and IFN-γ-induced genes in rat pancreatic β cells. Diabetologia 46: 1641-1657
43. Webb GC et al. (2000) Expression profiling of pancreatic β cells: glucose regulation of secretory and metabolic pathway genes. Proc Natl Acad Sci USA 97: 5773-5778
44. Scearce LM et al. (2002) Functional genomics of the endocrine pancreas: the pancreas clone set and PancChip, new resources for diabetes research. Diabetes 51: 1997-2004
45. Bernal-Mizrachi E et al. (2003) Gene expression profiling in islet biology and diabetes research. Diabetes Metab Res Rev 19: 32-42
46. Aune TM et al. (2003) Gene expression profiles in human autoimmune disease. Curr Pharm Des 9: 1905-1917
47. Gunton JE et al. (2005) Loss of ARNT/HIF1β mediates altered gene expression and pancreatic-islet dysfunction in human type 2 diabetes. Cell 122: 337-349
48. Mootha VK et al. (2003) PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34: 267-273
49. Subramanian A et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 15545-15550
50. Patti ME et al. (2003) Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: potential role of PGC1 and NRF1. Proc Natl Acad Sci USA 100: 8466-8471
51. Sreekumar R et al. (2002) Gene expression profile in skeletal muscle of type 2 diabetes and the effect of insulin treatment. Diabetes 51: 1913-1920
52. Whitfield ML et al. (2006) Common markers of proliferation. Nat Rev Cancer 6: 99-106
53. Sommer A and Haendler B (2003) Androgen receptor and prostate cancer: molecular aspects and gene expression profiling. Curr Opin Drug Discov Devel 6: 702-711
54. Eigl BJ et al. (2005) Timing is everything: preclinical evidence supporting simultaneous rather than sequential chemohormonal therapy for prostate cancer. Clin Cancer Res 11: 4905-4911
55. Novak K (2006) Where the chips fall. Nat Med 12: 158-159
56. Xu XQ et al. (2005) Gene expression profiling to identify oncogenic determinants of autocrine human growth hormone in human mammary carcinoma. J Biol Chem 280: 23987-24003
57. Hayashi S (2004) Prediction of hormone sensitivity by DNA microarray. Biomed Pharmacother 58: 1-9
58. Jaeger J et al. (2005) Early diagnostic marker panel determination for microarray based clinical studies. Stat Appl Genet Mol Biol 4: Article9
59. Carling T (2005) Multiple endocrine neoplasia syndrome: genetic basis for clinical management. Curr Opin Oncol 17: 7-12
60. Kim IJ et al. (2002) RET oligonucleotide microarray for the detection of RET mutations in multiple endocrine neoplasia type 2 syndromes. Clin Cancer Res 8: 457-463
61. Bowtell DD (1999) Options available - from start to finish - for obtaining expression data by microarray. Nat Genet 21: 25-32
62. Cheung VG et al. (1999) Making and reading microarrays. Nat Genet 21: 15-19
63. Haab BB et al. (2001) Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol [doi: 10.1186/gb-2001-2-2-research0004]
64. Hirschhorn JN and Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6: 95-108
65. Horikawa Y et al. (2000) Genetic variation in the gene encoding calpain-10 is associated with type 2 diabetes mellitus. Nat Genet 26: 163-175
66. Morley M et al. (2004) Genetic analysis of genomewide variation in human gene expression. Nature 430: 743-747