Fig. 6: Refined single sample PAM50 subtyping in ERpHER2n tumors based on leave-oneGeneCluster-out perturbation stable tumors.
From: Perturbation and stability of PAM50 subtyping in population-based primary invasive breast cancer
a Outline of the scheme to create refined ERpHER2n PAM50 centroids (termed PAM50K0) used for single sample classification by Spearman correlation based on FPKM values only (i.e., no gene centering). b Sankey plot of subtype change for ERpHER2n tumors when performing PAM50K0 classification as outlined in (a). c Kaplan–Meier plot of DRFI for PAM50K0 subtypes in endocrine-treated ERpHER2n tumors. d Boxplots of rank-based scores for the mitotic checkpoint, steroid response, and basal metagenes for endocrine-treated ERpHER2n tumors stratified by PAM50K0 subtypes. e Kaplan–Meier plot of DRFI for PAM50K0 subtypes in endocrine-treated ERpHER2n LumANC tumors. HER2EK0 and NormalK0 groups excluded due to size. f Left panel, Kaplan–Meier plot of OS for PAM50K0 subtypes in all endocrine-treated ERpHER2n LumANC tumors. HER2EK0 and NormalK0 groups excluded due to size. Right panel, same plot but only for non-K0 tumors (i.e., tumors not included in the PAM50K0 centroid creation). g Boxplots of rank-based scores for the mitotic checkpoint, steroid response, and basal metagenes for endocrine-treated ERpHER2n LumANC tumors stratified by PAM50K0 subtypes. Note that not all included cases in the study have DRFI outcome data, thus the difference in sample numbers between boxplots and survival plots. Boxplot elements correspond to: (1) center line = median, (2) box limits = upper and lower quartiles, (3) whiskers = 1.5x interquartile range.
