Probes specificity in array design influences the agreement between microarray and RNA-seq in gene expression analysis

More than a decade, oligonucleotide microarrays have been the method of choice for transcriptional profiling studies, used to characterize biological systems. The power of microarray platforms depends on the number, identity and specificity of the oligonucleotide probes for their target gene models. In recent time, however, researchers have been increasingly focusing high-throughput sequencing RNA-Seq which offers advantages when examining transcriptome fine structure; for example, in the detection of allele-specific expression and splice junctions. We are investigating how the specificity of oligonucleotide probes in an array design influences the agreement between RNA-Seq and microarray platforms in gene expression, differential analysis. Hence, we are essaying the agreement between a custom microarray platform, based on multiple long oligonucleotide probes (60 mer) per gene model transcript (Grape custom microarray platform), and RNA-Seq, by removing microarray, design less specific probes discriminating differential expressed genes (DEGs), analyzing two Vitis vinifera berry developmental stages. We were able to demonstrate that the agreement between both RNA-Seq and microarray platforms calling DEGs, depend on the high rate of probes set with specific oligonucleotide probes. Furthermore, this investigation confirmed the superiority of RNA-Seq next generation sequencing (NGS) technology, as opposed to microarray in gene expression differential analysis.