Fig. 4: Differential translation linked to differential splicing.

a ORF abundances were used to calculate an event relative abundance (RA) with SUPPA. b Correlation of splicing and translation changes in events. In red, significant cases in ribosome and RNA space (363); in black (493) or dark gray (227), cases significant only in one comparison; in light gray, nonsignificant cases. The bands show the density of cases along each axis. Empty circles indicate microexons. In blue, the correlation of the red points. In gray, the correlation of all other exons (black/dark gray/gray), both including microexons. c Differentially spliced events in RNA or ribosome space by event type: alternative 3′ss/5′ss (A3/A5), alternative first/last exon (AF/AL), mutually exclusive (MX) exon, retained intron (RI), and skipping exon (SE). In light gray, the proportion of SUPPA events calculated from annotated coding regions in human. In dark gray, the proportion of events with significant change between glia and glioma. There is enrichment of SE events in RNA (Fisher’s p-value 3.90e–06) and Ribo-seq (Fisher’s p-value 7.46e–07), of A3 events in RNA (Fisher’s p-value = 1.02e–05) and Ribo-seq (Fisher’s p-value 6.22e–06), of A5 events in RNA (Fisher’s p-value 4.55e–03) and Ribo-seq (Fisher’s p-value 8.73e–03), and significant depletion of AL events in RNA (Fisher’s p-value 1.73e−32) and Ribo-seq (Fisher’s p-value 2.43e−43) and of MX events in RNA (Fisher’s p-value 6.06e–04) and Ribo-seq (Fisher’s p-value 1.83e–03). d Enrichment of microexons with an impact on RNA splicing and ORF translation in glia vs glioma. dPSI denotes the difference in relative abundance in RNA or ribosome spaces. e dPSI values for high polysome fraction between neuronal samples and ESCs (y-axis) for microexons with significant change in ribosome space (x-axis). Box boundaries correspond to the first and third quartiles, the thick black line indicates the median, and top and bottom lines indicate the maximum and minimum values. Black dots represent all data points. f ORFs containing microexons detected only by ORQAS (orange), ORFquant (yellow), or both (blue). g Microexons (<52nt) and other SE events detected in ribosome space with PSI > 0.1 only by ORQAS (orange), by analyses from ref. ³¹ (green), or by both methods (blue).