Fig. 5: scRNA-Seq reveals non-coding transcriptional heterogeneity in melanoma 0D5P. | Nature Communications

Fig. 5: scRNA-Seq reveals non-coding transcriptional heterogeneity in melanoma 0D5P.

From: Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes

Fig. 5

a t-SNE plot of the 1365 cells colored by their “cell cycle” scores. b Examples of cell cycle dependent genes: ATAD2, a tumor-associated antigen, and c TMEM106C, from which a noncHLAIp originated. d Genes of interest were plotted based on their sum normalized expression by scRNA-Seq and ordered based on the percentage of cells that expressed the gene. The color codes denote the type of HLAIp identified from those genes. e t-SNE plot of the 1365 cells colored by the five identified clusters. Clusters were annotated based on functional enrichment analyses of marker genes. f t-SNE plot highlighting the expression of the ABCB5 gene enriched in cluster 0. g Heatmap showing the scaled and centered expressions of marker genes in cluster 0. The cluster colors from e are represented above the plot. h Expression profiles of four marker genes in cluster 0 over all other clusters, including two well-known cancer biomarkers, MITF and CTNNB1, and two source genes for which noncHLAIp were identified, the ABCB5 gene with a dORF and LINC00520. The p-values represented in b, c, and h were obtained with Wilcoxon tests. Source data are provided as a Source Data file.

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