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Fig 5 - Perturbation-response genes reveal signaling footprints in cancer gene expression

Response signatures outperform pathway methods for patient survival. a Pan-cancer associations between pathway scores and patient survival. Pathways on the horizontal axis and different methods on the vertical axis. Associations of survival increase (green) and decrease. Significance labels as indicated. Shades correspond to effect size, p values as indicated. b Volcano plot of cancers-specific associations between patient survival and inferred pathway score using PROGENy. Effect size on the horizontal axis. Below zero indicates increased survival (green), above decreased survival (red). FDRadjusted p values on the vertical axis. Size of the dots corresponds to number of patients in each cohort. c Kaplan-Meier curves of individual associations for kidney (KIRC), low-grade glioma (LGG), and adrenocortical carcinoma (ACC). Pathway scores are split in top and bottom quartiles and center half. Lines show the fraction of patients (vertical axis) that are alive at a given time (horizontal axis) within one year. P values for discretized scores
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