Fig. 1

Breast cancer intron retention in the TCGA cohort. A Overview of TCGA samples analysed. B Scatter plot illustrating the average number of IR events in cancers vs adjacent normal tissues. Error bars indicate standard deviations. The size of the dots is proportional to the number of samples analysed. C Bar plot showing the average number of IR events in normal tissues in descending order. Error bars represent standard error of the mean. D PCA plot showing clusters of specific IR profiles in ER positive and ER negative tumour samples (n = 509). E Distributions of IR event frequencies in four major BrCa subtypes (LumA—Luminal A; LumB—Luminal B; Basal, HER2—human epidermal growth factor receptor 2 positive). F Distributions of IR event frequencies in tumour samples assigned to three tumour stages. G Kaplan–Meier plot illustrating the survival probabilities of Luminal B BrCa patients stratified by a high vs low number of IR events. Samples have been dichotomized based on the median number of IR events