Fig. 5: Leave-oneGeneCluster-out perturbation and association to patient outcome.
From: Perturbation and stability of PAM50 subtyping in population-based primary invasive breast cancer
Forest plot of hazard ratios with 95% confidence intervals from univariate Cox regression, using DRFI as clinical endpoint, for tumors that switched subtype versus tumors that did not switch subtype (reference) after exclusion of a gene set in a TNBC tumors, b ERpHER2n tumors, and c endocrine-treated ERpHER2n tumors only. d Kaplan–Meier plot of DRFI for PAM50perturb subtypes in endocrine-treated ERpHER2n LumANC tumors after exclusion of gene set 1 (proliferation). e Kaplan–Meier plot of DRFI for PAM50perturb subtypes in endocrine-treated ERpHER2n LumBNC tumors after exclusion of gene set 3 (basal keratins). f Boxplots of rank-based scores for the mitotic progression, basal, steroid response, and lipid metagenes for endocrine-treated ERpHER2n LumANC tumors in panel (d). g Boxplots of rank-based scores for the mitotic progression, basal, steroid response, and lipid metagenes for endocrine-treated ERpHER2n LumBNC tumors in panel (e). 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.
