Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles

BACKGROUND: Several different microarray platforms are available for measuring gene expression. There are disagreements within the microarray scientific community for intra- and inter-platform consistency of these platforms. Both high and low consistencies were demonstrated across different platforms in terms of genes with significantly differential expression. Array studies for gene expression are used to explore biological causes and effects. Therefore, consistency should eventually be evaluated in a biological setting to reveal the functional differences between the examined samples, not just a list of differentially expressed genes (DEG). In this study, we investigated whether different platforms had a high consistency from the biologically functional perspective. RESULTS: DEG data without filtering the different probes in microarrays from different platforms generated from kidney samples of rats treated with the kidney carcinogen, aristolochic acid, in five test sites using microarrays from Affymetrix, Applied Biosystems, Agilent, and GE health platforms (two sites using Affymetrix for intra-platform comparison) were input into the Ingenuity Pathway Analysis (IPA) system for functional analysis. The functions of the DEG lists determined by IPA were compared across the four different platforms and two test sites for Affymetrix platform. Analysis results showed that there is a very high level of consistency between the two test sites using the same platform or among different platforms. The top functions determined by the different platforms were very similar and reflected carcinogenicity and toxicity of aristolochic acid in the rat kidney. CONCLUSION: Our results demonstrate that highly consistent biological information can be generated from different microarray platforms.