Fig. 1

Differential splicing across 16 distinct cancer types. The median numbers of (a) cassette exons, (b, c) alternative 5′ and 3′ splice sites, and (d) retained introns that are differentially spliced between patient-matched cancer and normal samples (y axis) versus log2 of the ratio of the number of events that are up- and downregulated in cancer versus normal controls (x axis). The median is computed across all samples for each cancer type. Upregulation is defined as increased cassette exon inclusion, usage of intron-proximal 5′ or 3′ splice sites, or increased intron retention. Bars indicate the standard deviation across samples for each cancer type, and circle sizes are proportional to the number of samples for each cancer type. See figure for color legend. (e, f) As panels A-D, but for (e) retention of constitutive introns or (f) alternative splicing of constitutive junctions. Upregulation is defined as increased constitutive intron retention or decreased alternative splicing of constitutive junctions. For constitutive introns, AML is outside the figure limits (to the right). (g) RNA-seq read coverage of CDK10 for a patient-matched cancer and normal sample from the colon. Shaded boxes mark introns that are most frequently retained in the cancer sample