Fig. 3

Contribution of cell types to differential editing. a Proportions of differentially edited (DE) genes from bulk tumor analysis that were expressed in cell types identified in lung cancer single-cell RNA-seq data. Each point represents the proportion of genes from one cancer type. A gene was considered as expressed in a cell type if its expression ≥ 1 RPKM. RPKM values were calculated within each cell type by pooling reads of the same cell type together. Proportions were compared for top cell types by Mann Whitney U test, with significance of p values shown. **p ≤ 0.01. EC stands for endothelial cells. b Proportion of differential editing sites from bulk tumor analysis that were edited in individual cell types. A site was considered as edited in a cell type if the site was covered by at least 5 reads and editing was supported by at least 2 reads. Each point represents the proportion of sites from one cancer type. Proportions for top cell types were compared by Mann Whitney U test, with p value significance shown. **p ≤ 0.01. c UMAP projection of 6526 tumor cells based on expression profiles, colored by cluster assignment (scatterplot, left). By differential expression of epithelial or mesenchymal markers (table, right), green and purple clusters were labeled as epithelial and mesenchymal, respectively. d Scatterplot of editing levels of pooled E and M cells, with y = x line. Editing sites exhibiting significant differences between E and M were labeled in red. Differences were considered significant if the difference between editing levels ≥ 0.05 and Fisher’s exact p value < 0.05