Validating nutrient-related gene expression changes from microarrays using RT 2 PCR-arrays

Genes and Nutrition

Volumn 3, Issue 3-4, 2008, Pages 153-157

  Gaj, S ^a,b   Eijssen, L ^b   Mensink, R P ^a,b   Evelo, C T A ^b  

^a TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^b MAASTRICHT UNIVERSITY   (Netherlands)

Author keywords

Human PBMC; Microarray; Nutrigenomics; QPCR; RT PCR; Validation

Indexed keywords

EID: 70349816126     PISSN: 15558932     EISSN: 18653499     Source Type: Journal    
DOI: 10.1007/s12263-008-0094-1     Document Type: Article

References (22)

1. Allanach K, Mengel M, Einecke G, Sis B, Hidalgo LG, Mueller T, Halloran PF (2008) Comparing microarray versus RT-PCR assessment of renal allograft biopsies: similar performance despite different dynamic ranges. Am J Transplant 8:1006-1015 (Pubitemid 351537773)
2. Allison DB, Cui X, Page GP, Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7:55-65 (Pubitemid 41828948)
3. Arikawa E, Sun Y, Wang J, Zhou Q, Ning B, Dial SL, Guo L, Yang J (2008) Cross-platform comparison of SYBR Green realtime PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the Micro- Array Quality Control (MAQC) study. BMC Genomics 9:328
4. Beckman KB, Lee KY, Golden T, Melov S (2004) Gene expression profiling in mitochondrial disease: assessment of microarray accuracy by high-throughput Q-PCR. Mitochondrion 4:453-470 (Pubitemid 39646798)
5. Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, Ma Y, Maqsodi B, Papallo A, Peters EH, Poulter K, Ruppel PL, Samaha RR, Shi L, Yang W, Zhang L, Goodsaid FM (2006) Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 24:1115-1122 (Pubitemid 44359723)
6. Dallas PB, Gottardo NG, Firth MJ, Beesley AH, Hoffmann K, Terry PA, Freitas JR, Boag JM, Cummings AJ, Kees UR (2005) Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR-how well do they correlate? BMC Genomics 6:59
7. Etienne W, Meyer MH, Peppers J, Meyer RA Jr (2004) Comparison of mRNA gene expression by RT-PCR and DNA microarray. BioTechniques 36:618-620, 622, 624-616
8. Fathallah-Shaykh HM (2005) Microarrays: applications and pitfalls. Arch Neurol 62:1669-1672 (Pubitemid 41626661)
9. Gaj S, van Erk A, van Haaften RI, Evelo CT (2007) Linking microarray reporters with protein functions. BMC Bioinformatics 8:360
10. Jellema A, Plat J, Mensink RP (2004) Weight reduction, but not a moderate intake of fish oil, lowers concentrations of inflammatory markers and PAI-1 antigen in obese men during the fasting and postprandial state. Eur J Clin Invest 34:766-773 (Pubitemid 39524302)
11. Mackay IM (2004) Real-time PCR in the microbiology laboratory. Clin Microbiol Infect 10:190-212 (Pubitemid 38379958)
12. Morey JS, Ryan JC, Van Dolah FM (2006) Microarray validation: factors influencing correlation between oligonucleotide microarrays and real-time PCR. Biol Proced Online 8:175-193 (Pubitemid 44942143)
13. Ning B, Dial S, Sun Y, Wang J, Yang J, Guo L (2008) Systematic and simultaneous gene profiling of 84 drug-metabolizing genes in primary human hepatocytes. J Biomol Screen 13:194-201 (Pubitemid 351322874)
14. Olofsson LE, Orho-Melander M, William-Olsson L, Sjoholm K, Sjostrom L, Groop L, Carlsson B, Carlsson LM, Olsson B (2008) C/EBP{alpha} in adipose tissue regulates genes in lipid and glucose metabolism and a genetic variation in C/EBP{alpha} is associated with serum levels of triglycerides. J Clin Endocrinol Metab (in press)
15. Park WD, Stegall MD (2007) A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds. BMC Genomics 8:88
16. Rajeevan MS, Ranamukhaarachchi DG, Vernon SD, Unger ER (2001) Use of real-time quantitative PCR to validate the results of cDNA array and differential display PCR technologies. Methods 25:443-451 (Pubitemid 34164016)
17. Smyth GK (2005) Limma: linear models for microarray analysis. In: Gentleman VCR, Dudoit S, Irizarry R, Huber W (eds) Bioinformatics and computational biology solutions using R and bioconductor. Springer, New York, pp 397-420
18. Svensson PA, Gabrielsson BG, Jernas M, Gummesson A, Sjoholm K (2008) Regulation of human aldoketoreductase 1C3 (AKR1C3) gene expression in the adipose tissue. Cell Mol Biol Lett 13(4):599-613
19. Wang Y, Barbacioru C, Hyland F, Xiao W, Hunkapiller KL, Blake J, Chan F, Gonzalez C, Zhang L, Samaha RR (2006) Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays. BMC Genomics 7:59
20. Wurmbach E, Yuen T, Sealfon SC (2003) Focused microarray analysis. Methods 31:306-316 (Pubitemid 37338768)
21. Yang YH, Speed T (2002) Design issues for cDNA microarray experiments. Nat Rev 3:579-588 (Pubitemid 34827132)
22. Yuen T, Wurmbach E, Pfeffer RL, Ebersole BJ, Sealfon SC (2002) Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res 30:e48