Fig. 2: IR represents a consistent hallmark of PCa stemness and progression.

a–d Changes in IR and SE across the 14 comparisons detected by rMATS. Both clinical (a–c) and experimental (d) RNA-seq datasets were used. The data were presented as fold changes in a comparative manner and baseline refers to 1. e RBP motif analysis of retained introns specific to the PCa stages indicated. A total of 95 RBPs are examined and shown are the top 20 genes ranked by a binding score that takes into account both binding frequency and binding strength for each RBP. f DSEs associated with high or low expression level of ELAVL1 and RBM38 in pri-PCa and CRPC-Ad, respectively. g Pairwise comparison of expression of the genes showing significant IR events during PCa progression. Expression variability is quantified for each gene as a Z-score relative to the mean expression in normal prostate samples. Genes exhibiting both up- and downregulated IR events are removed, and the resultant gene number is indicated. Within the plots, the center lines represent median values, box edges are 75th and 25th percentiles, and whiskers denote the maximum and minimum values, respectively. Significance was calculated by two-tailed paired Student’s t-test (NS, not significant). h Overlap of significant IR-bearing genes with a high-confidence set of 1000 human NMD targets. Significance was calculated by two-tailed χ²-test (NS, not significant). DSEs, differentially spliced events; RBP, RNA-binding protein; NMD, nonsense-mediated mRNA decay. Source data are provided as a Source Data file.