Figure 1: Design and workflow for integrative analysis combining germline with somatic mutation information using gene expression data. RNA-seq read count data and somatic information were downloaded from The Cancer Genome Atlas (TCGA) via the Genomics Data Commons. Germline mutation information was manually curated from GWAS studies. Limma (R) package was used for the discovery of differentially expressed (DE) mutated and nonmutated genes. Ingenuity Pathway Analysis (IPA) was used for functional analysis and discovery of molecular networks and biological pathways enriched for germline and somatic mutations.