Comparative analysis of oncogenes identified by microarray and RNA-sequencing as biomarkers for clinical prognosis

Abstract

Aims: Although RNA-sequencing has been widely used to identify the differentially expressed genes (DEGs) as biomarkers to guide the therapeutic treatment, it is necessary to investigate the concordance of DEGs identified by microarray and RNA-sequencing for the clinical prognosis. Material & methods: By using The Cancer Genome Atlas data sets, we thoroughly investigated the concordance of DEGs identified from microarray and RNA-sequencing data and their molecular functions. Results: The DEGs identified by both technologies averaged ˜98.6% overlap. The cancer-related gene sets were significantly enriched with the DEGs and consistent between two technologies. Conclusions: The highly consistency of DEGs in their regulation directionality and molecular functions indicated the good reproducibility between microarray and RNA-sequencing in identifying potential oncogenes for clinical prognosis.