Comparison of the main Penelope-derived gene clusters with the three established gene signatures RS, GGI and SET. The gene clusters from the Penelope-B analysis (as shown inFigure 3) were analyzed in RNA-seq data of 812 ER positive breast cancer samples from TCGA for their correlation to established gene signatures (recurrence score, GGI, and SET-index) as shown in the scatterplots. Scatterplots with Pearson correlation values R > 0.5 are highlighted: Both recurrence score (R = 0.827) and GGI (R = 0.991) display strong correlation with gene cluster 2 (cell cycle/proliferation) from the Penelope-B analysis. Subcluster 1C from the Penelope-analysis which was characterized by estrogen responsive genes displays a strong correlation (R = 0.805) with the SET-index. Calculation of RS30and GGI31were adapted from genefu package67, and SET32from Sinn 2019.68Detailed code is provided in thesupplemental information.
