Kaplan–Meier survival analysis using TCGA RNA seq database

RNA-seq data was downloaded from The Cancer Genome Atlas (TCGA) for head and neck squamous cell carcinoma (HNSC, n = 520). Samples were stratified to low and high expression of GNA13 based on median expression of the gene, and compared for survival and stemness or EMT. Individual gene signatures were selected from the molecular signatures database (MSigDB) portal, genes representing stemness (MSigDB ref: M9473) and EMT (MSigDB ref: M5930) were used. The expression of genes in each of these signatures was displayed as a heatmap. Overall survival was compared between groups and a boxplot used to visualize the distribution of GNA13 expression in each group. All data analysis was carried out using R 3.2.2 (R: A Language and Environment for Statistical Computing. R Core Team. 2016 https://www.R-project.org). TCGA RNA-seq data was downloading using the RTCGA package (Marcin Kosinski and Przemyslaw Biecek (2016). RTCGA: The Cancer Genome Atlas Data Integration. R package version 1.1.14.) and converted to Log2-CPM (counts per million) utilizing the voom function in the limma package as described in [52]. Survival curves were compared using the Mantel–Haenszel test.