Faculty Collaboration Database

Three-color cDNA microarrays with prehybridization quality control yield gene expression data comparable to that of commercial platforms. Physiol Genomics 2006 Mar 13;25(1):166-78

Date

01/13/2006

Pubmed ID

16403843

DOI

10.1152/physiolgenomics.00243.2005

Scopus ID

2-s2.0-33645766760 (requires institutional sign-in at Scopus site)   5 Citations

Abstract

Despite their lower cost and high content flexibility, a limitation of in-house-prepared arrays has been their susceptibility to quality control (QC) issues and lack of QC standards across laboratories. Therefore, we developed a novel three-color array system that allows prehybridization QC as well as the Matarray software to facilitate acquisition of accurate gene expression data. In this study, we compared performance of our rat cDNA array to the Affymetrix RG-U34A and Agilent G4130A arrays using 2,824 UniGenes represented on all three arrays. Before data filtering, poor interplatform agreement was observed; however, after data filtering, differentially expressed UniGenes exhibited correlation coefficients of 0.91, 0.88, and 0.92 between the Affymetrix vs. Agilent, Affymetrix vs. cDNA, and Agilent vs. cDNA arrays, respectively. The Affymetrix, Agilent, and cDNA arrays agreed well with quantitative RT-PCR conducted on 42 UniGenes, yielding correlation coefficients of 0.90, 0.90, and 0.96, respectively. Each platform underestimated ratios relative to quantitative RT-PCR, possessing respective slopes of 0.86 (R2 = 0.81), 0.65 (R2 = 0.81), and 0.70 (R2 = 0.92). Overall, these data show that the combination of our novel technical and analytic approaches yield an accurate platform for functional genomics that is concordant with commercial discovery arrays in terms of identifying regulated genes and pathways.

Author List

Hessner MJ, Xiang B, Jia S, Geoffrey R, Holmes S, Meyer L, Muheisen S, Wang X

Author

Martin J. Hessner PhD Professor in the Pediatrics department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Analysis of Variance
Animals
Gene Expression Profiling
Gene Expression Regulation
Indicators and Reagents
Liver
Nucleic Acid Hybridization
Oligonucleotide Array Sequence Analysis
Quality Control
Rats
Rats, Inbred BB
Rats, Inbred WF
Reproducibility of Results