RNA-Seq and Microarray Gene Expression Vie for Superiority within a Comprehensive Study Design. Rattus norvegicus strain:Sprague-Dawley

The comparative advantages of RNA-Seq and microarrays in transcriptome profiling were evaluated in the context of a comprehensive study design. Gene expression data from Illumina RNA-Seq and Affymetrix microarrays were obtained from livers of rats exposed to 27 agents that comprised of seven modes of action (MOAs); they were split into training and test sets and verified with real time PCR. RNA-Seq edged microarray in detecting differential expression, particularly for low abundance mRNAs. The concordance (20% - 60%) depends on the nature of the samples and is improved when the top 50% expressed genes are used in the comparison (~70%). Nonetheless, both platforms profiled co-regulated genes similarly and derived gene signatures with comparable MOA prediction accuracy (~60%). By placing an emphasis on the commonly detected genes, RNA-Seq seems to provide comparable or better transcriptomic profiling as compared with the standard microarray technology for the elucidation of biological responses to perturbations.