Evaluation of microarray sensitivity and specificity in gene expression differential analysis by RNA-Seq and quantitative RT-PCR

There are several techniques for quantifying the amount of transcribed mRNA, all of them relying on the fundamental property of complementary base pairing. The widely used tools are gene expression microarrays, allowing for the snapshot of the entire genome. The reliability of microarray technology in gene expression analysis and diagnostic process have been fully discussed and critiqued, allowing the development of several microarray technology design strategies with the aim of improving its accuracy in transcriptome and genomic studies. Hence, we are evaluating the sensitivity and the specificity of four previously developed grape microarray design strategies based either on multiple and/or single long and/or short oligonucleotide probe per gene model transcript by RNA-Seq and quantitative RT-PCR (qRT-PCR) technologies; this is due to their advantages in detection sensitivity, sequence specificity, the large dynamic as well as their high precision and reproducible quantitation compare to microarray. Our results showed that (i) regardless of the array design strategies used, microarray gene expression technologies are less specific and less sensitive for the purpose of detecting lower expressed gene (differential expressed genes (DEGs)) associated with small variation change; and (ii) for the highly expressed genes, microarray gene expression platforms, exhibited a high reliability and a good level of agreement with both RNA-Seq and qRT-PCR tools in gene expression differential analysis.