Microarray validation: Factors influencing correlation between oligonucleotide microarrays and real-time PCR

Biological Procedures Online

Volumn 8, Issue 1, 2006, Pages 175-193

  Morey, Jeanine S ^a,b   Ryan, James C ^a   Van Dolah, Frances M ^a  

^a CENTER FOR COASTAL ENVIRONMENTAL HEALTH AND BIOMOLECULAR RESEARCH   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AZASPIRACID; BREVETOXIN; DOMOIC ACID;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA MICROARRAY; DOWN REGULATION; FEMALE; GENE CONTROL; GENE EXPRESSION; HUMAN; HUMAN CELL; INFORMATION PROCESSING; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; QUALITY CONTROL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; STATISTICAL SIGNIFICANCE; TLYMPHOCYTE; UNINDEXED SEQUENCE; UPREGULATION; VALIDATION STUDY;

EID: 33845624887     PISSN: 14809222     EISSN: None     Source Type: Journal    
DOI: 10.1251/bpo126     Document Type: Article

References (28)

1. Bustin S. Invited review: quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol 2002; 29:23-39.
2. Chuaqui RF, Bonner RF, Best CJM, Gillespie JW, Flaig MJ, Hewitt SM, Phillips JL, Krizman DB, Tangrea MA, Ahram M, Linehan WM, Knezevic V, Emmert-Buck MR. Post-analysis follow-up and validation of microarray experiments. Nat Genet 2002; 32:509-514.
3. Freeman WM, Walker SJ, Vrana KE. Quantitative RT-PCR: pitfalls and potential. BioTechniques 1999; 26:112-125.
4. Wurmbach E, Yuen T, Sealfon SC. Focused microarray analysis. Methods 2003; 31:306-316.
5. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucl Acids Res 2002; 30(4):e15.
6. Barrett JC, Kawasaki ES. Microarrays: the use of oligonucleotides and cDNA for the analysis of gene expression. Drug Discov Today 2003; 8:134.
7. Brazeau DA. Combining genome-wide and targeted gene expression profiling in drug discovery: microarrays and real-time PCR. Drug Discov Today 2004; 9:838-845.
8. Bustin S. Review: absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 2000; 25:169-193.
9. Mah N, Thelin A, Lu T, Nikolaus S, Kuhbacher T, Gurbuz Y, Eickhoff H, Kloppel G, Lehrach H, Mellgard B, Costello CM, Schreiber S. A comparison of oligonucleotide and cDNA-based microarray systems. Physiol Genomics 2004; 16:361-370.
10. Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC. Evaluation of gene expression measurements from commercial microarray platforms. Nucl Acids Res 2003; 31:5676-5684.
11. Yauk CL, Berndt ML, Williams A, Douglas GR. Comprehensive comparison of six microarray technologies. Nucl Acids Res 2004; 32:e124.
12. Zhu B, Ping G, Shinohara Y, Zhang Y, Baba Y. Comparison of gene expression measurements from cDNA and 60-mer oligonucleotide microarrays. Genomics 2005; 85:657-665.
13. Bustin SA. Quantification of nucleic acids by PCR. In Bustin SA, editor. A-Z of Quantitative PCR. La Jolla, CA: International University Line; 2004. p. 3-46.
14. Beckman KB, Lee KY, Golden T, Melov S. Gene expression profiling in mitochondrial disease: assessment of microarray accuracy by high-throughput Q-PCR. Mitochondrion 2004; 4:453.
15. Etienne W, Meyer MH, Peppers J, Meyer RA Jr. Comparison of mRNA gene expression by RT-PCR and DNA microarray. BioTechniques 2004; 36:618-621.
16. Larkin JE, Frank BC, Gaspard RM, Duka I, Gavras H, Quackenbush J. Cardiac transcriptional response to acute and chronic angiotensin II treatments. Physiol Genomics 2004; 18:152-166.
17. Rajeevan MS, Ranamukhaarachchi DG, Vernon SD, Unger ER. Use of real-time quantitative PCR to validate the results of cDNA array and differential display PCR technologies. Methods 2001; 25:443-451.
18. Svaren J, Ehrig T, Abdulkadir SA, Ehrengruber MU, Watson MA, Milbrandt J. EGR1 target genes in prostate carcinoma cells identified by microarray analysis. J Biol Chem 2000; 275:38524-38531.
19. Rajeevan MS, Vernon SD, Taysavang N, Unger ER. Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR. J Mol Diagn 2001; 3:26-31.
20. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotech 2001; 19:342-347.
21. Li J, Pankratz M, Johnson JA. Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol Sci 2002; 69:383-390.
22. Ryan JC, Morey JS, Ramsdell JS, Van Dolah FM. Acute phase gene expression in mice exposed to the marine neurotoxin domoic acid; excititoxicity stimulates ischemia. Neuroscience 2005; 136:1121-1132.
23. Twiner MJ, Hess P, Bottein Dechraoui M-Y, McMahon T, Ramsdell JS, Samons MS, Satake M, Yausumoto T, Doucette GJ. Cytotoxic and cytoskeletal effects of azaspiracid-1 on multiple mammalian cell lines. Toxicon 2005; 45:891-900.
24. Williams TD, Gensberg K, Minchin SD, Chipman JK. A DNA expression array to detect toxic stress response in European flounder (Platichthys flesus). Aquat Toxicol 2003; 65:141-157.
25. Dallas PB, Gottardo NG, Firth MJ, Beesley AH, Hoffmann K, Terry PA, Freitas JR, Boag JM, Cummings AJ, Kees UR. Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time PCR - how well do they correlate? BMC Genomics 2005; 6(1):59.
26. Johnson SA, Morgan DG, Finch CE. Extensive postmortem stability of RNA from rat and human brain. J Neuroscience Res 1986; 16:267-280.
27. Karsten SL, Van Deerlin VM, Sabatti C, Gill LH, Geschwind DH. An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucl Acids Res 2002; 30(2):e4.
28. Van Deerlin VM, Gill LH, Nelson PT. Optimizing Gene Expression Analysis in Archival Brain Tissue. Neurochemical Research 2002; 27:993-1003.