Fig. 4: Intronic APA is associated with clinical variables.

a Boxplots present four examples where intronic APA events are associated with hormone receptor phenotypes but not with the corresponding gene expression levels in BRCA data. The significance of these associations was assessed using unpaired t tests, and the p values were as follows: SNX5 TR p = 6.24e-18, gene expression (GE) p = 0.529; TP53RK TR p = 1.02e-16, GE p = 0.851; CNOT6L TR p = 4.65e-6, GE p = 0.922; SYNGR1 TR p = 1.05e-27, GE p = 0.701. b Violin plots illustrating two exemplary genes demonstrating significant intronic APA events but not significant differential gene expression in cancer stages. c Kaplan‒Meier (KM) plots illustrating the correlation between the TR of PHF19 and the disease-free rate or survival rate of HNSC and KIRC patients. d KM plots for the high- (red line) and low-risk (blue line) groups generated based on gene expression, TR of intronic APA events, and the combination of gene expression and TR. The upper three KM plots represent case 1, and the lower three KM plots represent case 2. The p values were determined using the log-rank test. e Prediction results of hormone receptor phenotypes based on gene expression, TR of intronic APA events, and the combination of gene expression and TR. SVM was used for the prediction task, and the mean AUC of 100 repeats (i.e., splitting of trainings, validation, and test sets) is reported.