Microarray platforms - Comparisons and contrasts

Pharmacogenomics

Volumn 5, Issue 5, 2004, Pages 487-502

  Hardiman, Gary ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Data integration; Expression platforms; Microarray technology; Oligonucleotide chips

Indexed keywords

COMPLEMENTARY DNA; DNA; FLUORESCENT DYE; MESSENGER RNA; OLIGONUCLEOTIDE; PHYCOERYTHRIN; POLYADENYLATED RNA; RIBONUCLEASE; STREPTAVIDIN;

ACCURACY; ANALYTIC METHOD; COMPARATIVE STUDY; COMPUTER PROGRAM; CYTOLOGY; DATA ANALYSIS; DNA MICROARRAY; DNA PROBE; DNA SYNTHESIS; EXPERIMENTATION; GENE AMPLIFICATION; GENE EXPRESSION; GENE SEQUENCE; GENE TARGETING; GENE TECHNOLOGY; GENETIC ANALYSIS; GENETIC DATABASE; HUMAN; INFORMATION PROCESSING; MATHEMATICAL GENETICS; MEDICAL INSTRUMENTATION; MOLECULAR BIOLOGY; NONHUMAN; NORTHERN BLOTTING; POLYMERASE CHAIN REACTION; PUBLICATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SCIENTIFIC LITERATURE; STATISTICAL ANALYSIS;

HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 3543068702     PISSN: 14622416     EISSN: None     Source Type: Journal    
DOI: 10.1517/14622416.5.5.487     Document Type: Review

References (42)

1. Chee M, Yang R, Hubbell E et al.: Accessing genetic information with high-density DNA arrays. Science 274, 610-614 (1996).
2. Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995).
3. Pomeroy SL, Tamayo P, Gaasenbeek M et al.: Prediction of central nervous system embryonal tumor outcome based on gene expression. Nature 415, 436-442 (2002).
4. van't Veer LJ, Dai H, van de Vijver MJ et al.: Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536 (2002).
5. Marton MJ, DeRisi JL, Bennett HA et al.: Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat. Med. 4, 1293-1301 (1998).
6. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM: Systematic determination of genetic network architecture. Nat. Genet. 22, 281-285 (1999).
7. Waring JF, Ciurlionis R, Jolly RA, Heindel M, Ulrich RG: Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol. Lett. 120, 359-368 (2001).
8. DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686 (1997).
9. Iyer VR, Eisen MB, Ross DT et al.: The transcriptional programme in the response of human fibroblasts to serum. Science 283, 83-87 (1999).
10. Hughes TR, Marton MJ, Jones AR et al.: Functional discovery via a compendium of expression profiles. Cell 102, 109-126 (2000).
11. Chuaqui RF, Bonner RF, Best CJ et al.: Postanalysis follow-up and validation of microarray experiments. Nat. Genet. 32, 509-514 (2002).
12. Brazma A, Hingamp P, Quackenbush J et al.: Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat. Genet. 4, 365-371 (2001).
13. Kerr MK, Churchill GA: Experimental design for gene expression microarrays. Biostatistics 2, 183-201 (2001).
14. Gaasterland T, Bekiranov S: Making the most of microarray data. Nat. Genet. 24, 204-206 (2000).
15. Stafford P. Liu P: Microarray technology comparison, statistical analysis, and experimental design. In: Microarray Methods and Applications - Nuts and Bolts. DNA Press, Eagleville, PA, USA 273-324 (2003).
16. Bowtell DDL: Options available - from start to finish for obtaining expression data by microarray. Nat. Genet. 21, 25-32 (1999).
17. Hardiman G: Microarray technologies 2003 - an overview. Pharmacogenomics 4, 251-256 (2003).
18. Knight J: When the chips are down. Nature 410, 6831 (2001).
19. Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ: High density synthetic oligonucleotide arrays. Nat. Genet. 21(Suppl.), 20-24 (1999).
20. Hughes TR, Mao M, Jones AR et al.: Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotech. 19, 342-347 (2001).
21. Southern E, Mir K, Shchepinov M: Molecular interactions on microarrays. Nat. Genet. 21(Suppl.), 5-9 (1999).
22. Shchepinov MS, Case-Green SC, Southern EM: Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 25, 1155-1161 (1997).
23. Ramakrishnan R, Dorris D, Lublinsky A et al.: An assessment of Motorola CodeLink™ microarray performance for gene expression profiling applications. Nucleic Acids Res. 30, E30 (2002).
24. Nuwaysir EF, Huang W, Albert TJ et al.: Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12, 1749-1755 (2002).
25. Baum M, Bielau S, Rittner N et al.: Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling. Nucleic Acids Res. 31(23), E151 (2003).
26. Puskas LG, Zvara A, Hackler L Jr, Micsik T, van Hummelen P: Production of bulk amounts of universal RNA for DNA microarrays. Biotechniques 33, 898-904 (2002).
27. Dudley AM, Aach J, Steffen MA, Church GM: Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range Proc. Natl. Acad. Sci. USA 99, 7554-7559 (2002).
28. Yang YH, Dudoit S, Luu P et al.: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, E15 (2002).
29. GeneChip™ eucaryotic small sample target labelling assay version II. Affymetrix technical note (2002).
30. Moreau Y, Aerts S, De Moor B, de Strooper B, Dabrowski M: Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet. 10, 570-577 (2003).
31. Taniguchi M, Miura K, Iwao H, Yamanaka S: Quantitative assessment of DNA microarrays - comparison with northern blot analyses. Genomics 71, 34-39 (2001).
32. Al Moustafa AE, Alaoui-Jamah MA, Batist G et al.: Identification of genes associated with head and neck carcinogenesis by cDNA microarray comparison between matched primary normal epithelial and squamous carcinoma cells. Oncogene 21, 2634-2640 (2002).
33. Jia MH, LaRossa RA, Lee J-M et al.: Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl. Physiol. Genomics 3, 83-92 (2000).
34. Kothapalli R, Yoder SJ, Mane S, Loughran TP: Microarray results: how accurate are they? Bioinformatics 3, 22 (2002).
35. Tsai J, Sultana S, Lee Y et al.: J. Genome Biol. 2, software0002.1-0002.4 (2001).
36. Diehn M, Sherlock G, Binkley G et al.: SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 31, 219-223 (2003).
37. Kuo WP, Jenssen TK, Butte AJ, Ohno-Machado L, Kohane IS: Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18, 405-412 (2002).
38. Li J, Pankratz M, Johnson JA: Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol. Sci. 69, 383-390 (2002).
39. Tan PK, Downey TJ, Spitznagel EL Jr et al.: Evaluation of gene expression measurements from commercial microarray platforms. Nucl. Acids. Res. 31, 5676-5684 (2003)
40. Barczak A, Rodriguez MW, Hanspers K et al.: Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res. 13, 1775-1785 (2003).
41. Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM: Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res. 62, 4427-4433 (2002).
42. Choi JK, Yu U, Kim S, Yoo OJ: Combining multiple microarray studies and modeling interstudy variation. Bioinformatics 19(Suppl. 1), i84-i90 (2003).