In this study, we evaluated perturbations in transcriptome landscapes as a function of the disease (breast vs. ovarian cancers), the gene (BRCA1 vs. BRCA2), and the mutation type (somatic vs. germline) by applying a multilayer self-organizing maps approach on the next generation RNA-sequencing data from TCGA-OC and TCGA-BRCA projects. Here, BRCA2 is linked to ovarian cancer.