Fig. 2

Intron retention characterizes all analyzed cancer types except for breast. (a) Numbers of introns with increased or decreased retention in cancer versus control normal samples in AML, colon cancer, and breast cancer. Red/blue illustrate cancer samples that exhibit an enrichment >1.5-fold for increased/decreased intron retention relative to control normal samples. (b) The average number of differentially retained introns versus the mean absolute change in retention level, computed for each cancer type. Error bars indicate standard deviation across the individual patient samples. Colors as Fig. 1. (c) Median log2 of the ratio of the number of introns that exhibit increased and decreased retention in cancer versus normal controls, where the median is taken over all samples for each cancer type. The x and y axes are, respectively, restricted to annotated alternative and constitutive introns. Colors as Fig. 1. (d) As Fig. 1d, but computed using only reads crossing the exon-intron boundary. (e) Median log2 of the ratio of the number of introns that exhibit increased and decreased retention in normal breast versus other normal control tissues (x axis), and breast cancer versus other cancer types (y). (f) Number of differentially retained introns in breast cancer cell lines (gray) compared to non-cancerous epithelial breast cells (red). Triangles [23]; circles [24]