Fig. 4

Comparison of splicing category distributions between iPS and endoderm cells. a Pie chart showing the number of category switches between iPS and endoderm cells (left panel). The zoom-in (right panel) shows details of different category switches. The outer pie chart shows the splicing category of each cassette exon at the iPS state and the internal pie chart shows the respective category at endoderm state. Non-annotated slices in the pie chart reflect ~ 1% of the data. b DNA methylation changes associated with the observed category switches. The top panel shows the iPS and endoderm splicing categories colored according to a. The bottom panel shows DNA methylation levels within the seven sequence contexts of a cassette exon as compared to the DNA methylation levels of the cassette exons that do not switch in their splicing category. Significant changes (Q < 0.05) are marked with a star. DNA methylation of the alternative exon and its vicinity is increased in cassette exons that switch from the underdispersed category. Cassette exons that switch from either included or excluded to any other splicing category show increased DNA methylation of the upstream exon (C1). c Performance of logistic ridge regression models that predict the absence/presence of switching splicing categories between iPS and endoderm states. DNA methylation information improves the prediction of the under- and overdispersed cassette exons. The categories are colored according to a. Error bars denote ± 1 standard deviation across four repeat experiments