Fig. 6: RNA-only and clinical + RNA models of overall survival in patients with stage II-III TNBC.

a–c corresponds to the RNA-only elastic net model, and d–f corresponds to the clinical + RNA elastic net model. a, d The features selected by the elastic net model and their corresponding scaled coefficient values. Features with negative values (blue) are associated with better overall survival and features with positive values (red) are associated with worse overall survival. b, e Kaplan–Meier plots of overall survival by predicted survival risk from the corresponding elastic net model. Continuous risk scores predicted for each sample were categorized into low-risk (blue), medium-risk (black), and high-risk (red) cutoffs based on the median risk score of each test set. Samples and associated risk scores from the three test sets were combined. c, f The likelihood-ratio (LR) statistic was estimated as we added the continuous elastic net risk score and/or tumor stage to a Cox proportional hazards model using the samples from the combined test set. The change in LR statistic when tumor stage, then risk score is added is shown (order 1) alongside the change in LR statistic when RNA model risk, then tumor stage is added is shown (order 2). The p-values displayed represent the statistical significance of the corresponding coefficient in the univariate/multivariate model on test set data.