Figure 4: Inhibition and modulation of the effect of E7107 on global splicing patterns by PHF5A-Y36C.

(a) Stacked bar graph of the counts (left panel) and fractions (right panel) of differential splicing events in each indicated treatment group as compared to DMSO controls. (b) Summary of the counts and log₂ fold changes of differential splicing events in the indicated treatment group as compared to DMSO controls. Box shows the interquartile range (IQR) of the data set whereas the whiskers illustrate 1.5 × IQR. (c) Plot of average GC content within retained introns and downstream exons from E7107-induced intron-retention junctions. Each intron was normalized to 100 bins whereas each exon to 50 bins (see Methods for details). Dark line represents average GC content of each bin; shaded region indicates the 95% confidence interval. (d) Plot of average GC content within skipped-exons and both upstream (left) and downstream (right) introns from E7107-induced exon-skipping junctions. Each intron was normalized to 100 bins whereas each exon to 50 bins (see Methods for details). Dark line represents average GC content of each bin; shaded region indicates the 95% confidence interval. (e) Waterfall plot of the 3′ junction usage of 3,883 junctions (see text for details) in E7107 treated PHF5A Y36C (top) and WT (bottom) cells. X axis on both panels is ordered based on the ES PSI (percentage spliced in) value (large to small) of each junction in E7107-treated Y36C line. On y axis the PSI of either exon-skipping (ES, blue) or intron-retention (IR, green) of the same 3′ junction were shown. The scheme of PSI calculation is shown below waterfall plots.