Fig. 4

Single-cell proteogenomic analyses. a–g Canonical (n = 1702) and non-canonical MAPs (ncRNA (378), intronic (114), and EREs (232)) were searched with BamQuery in bam files of scRNA-seq of normal and cancerous lung samples in single-cell in stranded mode with genome version GRCh38.p13, gene set annotations release v38_104, and dbSNP release 151. a Median percentage of MAPs detected in normal and cancerous lung scRNA-seq, as well as in bulk RNA-seq samples of normal lungs from GTEx (n = 150). b Number of canonical MAPs located in the 5′ (first half of the transcript) or 3′ (second half of the transcript) region of the transcript detected in indicated scRNA-seq datasets. c Median percentage of indicated MAP groups detected in normal and cancerous lung scRNA-seq, as well as in bulk RNA-seq samples of normal lungs from GTEx. d Number of MAPs identified as differentially expressed by the different populations of cells in the normal lung (left panel) or cancerous lung (right panel). The originally reported biotype of the MAPs is indicated by the color code. e TSNE analysis of the hematopoietic (blue) and stromal (orange) cells from the normal lung based on their MAP expression. f Heatmap showing the co-expression (spearman rho, color bar) of MAPs overexpressed by lung cancer cells (rows vs. columns). Two clusters of MAPs are highlighted on the left side of the heatmap (cluster 1 and cluster 2). g TSNE showing the expression of MAPs (color bar) from cluster 1 (higher panel) or cluster 2 (lower panel). Grey color indicates the null expression of a MAP in a cell