Fig. 4

Differential APA analysis of single-cell data by MAAPER. A Outline of APA analysis of placental data (10x Genomics) using MAAPER. B tSNE plot of the three trophoblast cell types based on gene expression in the Vento-Tormo et al. data. C Number of genes with a varying number of predicted PASs based on the Vento-Tormo et al. data. Bars denote the average gene number across three cell types; error bars denote SD. D Proportions of predicted PASs and nearSite reads based on their genomic positions. Proportions were averaged across all Vento-Tormo et al. samples. E Distributions of REDu scores calculated for EVTs vs. VCTs (left) and SCTs vs. VCTs (right). The 1st trimester (Vento-Tormo et al.) results are shown on the top, and the 3rd trimester (Tsang et al.) results at the bottom. Only genes that showed significant APA changes in the corresponding samples are included. F Sankey plots showing APA changes between the two trimesters in EVTs vs. VCTs (left) or SCTs vs. VCTs (right). Gene numbers are marked on the two sides of the Sankey plots. Genes are categorized as lengthened or shortened based on REDu scores (genes without significant changes are labeled as “unchanged”). Only genes with significant changes in at least one condition, either 1st trimester or 3rd trimester, are shown. S/L = no. of genes showing 3′UTR shortening/no. of genes showing 3′UTR lengthening. G As in E, except that REDi scores are shown