Fig. 3

Subtype characterization with MethCORR inferred RNA expression. a Scatterplot with correlation between normalized enrichment scores (NESs) from a gene set enrichment analysis (GSEA) of the TCGA BRCA Basal-like subtype vs. all other BRCA samples (HER2-enriched, Luminal, and normal-like) performed with RNA expression (x-axis) or iRNA expression (y-axis). b Scatterplot with correlation between NESs from a GSEA of the TCGA BRCA Basal-like subtype vs. all other BRCA samples performed with iRNA expression as input (x-axis) and the Basal-like subtype vs. all other samples in the independent FFPE cohort (GSE117439) performed with iRNA expression as input (y-axis). c Table with selected gene sets differentially enriched between breast cancer subtypes identified by GSEA analysis. GSEA was performed with RNA and iRNA expression in the TCGA BRCA cohort and iRNA expression in the independent breast cancer FFPE cohort (GSE117439). Gene sets with a positive NES are indicated by a red color scale and gene sets with a negative NES are indicated by a blue color scale. Significance is highlighted by bold (FDR < 0.05). See the methods section for the origin of the selected gene sets. d Scatterplot with correlation between ESTIMATE immune scores from an ESTIMATE [46] analysis performed with RNA expression (x-axis) or iRNA expression (y-axis). e Kaplan–Meier plots showing the overall survival of AJCC stage I-IV ER positive patients from the TCGA BRCA cohort stratified according to high or low CD8A expression (median cut-off) using either RNA (left panel) or iRNA (right panel). Significance was evaluated by the log-rank test. f Line chart with correlations between enrichment scores from single sample GSEA performed with RNA expression in fresh-frozen tissue and iRNA expression calculated in matched FFPE tissue or RNA expression in matched FFPE tissue. Correlations are shown for all samples with matched tissue for the BRCA (n = 3), PRAD (n = 3), LUAD (n = 9), BLCA (n = 3), KIRC (n = 3), and UCEC (n = 4) cohorts