TCGA subtype analysis.

The TCGA-KIRC cohort of 309 white males was used to determine the pattern of stratification by MG-154 signature. cBioportal (https://www.cbioportal.org/study/summary?id=kirc_tcga, Firehose Legacy) was used to extract sample-specific metadata, including overall survival and mutational profiles, whereas normalized RNA-Seq expression profiles were obtained using iLINCS (http://www.ilincs.org/ilincs/dataset/TCGA_KIRC_RNA-seqV2). The strata observed using the MG-154 signature and differential coexpression analysis were characterized in terms of stage, grade, survival, and mutational status. The R package Survival and cBioportal were used to generate Kaplan-Meier curves and assess statistical significance of differences in overall survival using a log-rank test. A χ2 test was used to determine differences in frequencies of stage, grade, and metastatic status of the subtypes. Subtypes observed in CTSC were mapped into TCGA subtypes using the nearest centroid analysis with Euclidean distance, where centroids for each TCGA subtype were defined as arithmetic averages of gene expression within each subtype, and each sample in the CTSC discovery cohort was mapped to the TCGA subtype centroid with the smallest distance.