Figure 8

Increased contaminating cytotoxic T-cells are unlikely to account for altered expression of OXPHOG gene levels in cluster 1 tumor samples. The fold-change in geometric means for all 118 OXPHOG genes expected for a mixed theoretical sample consisting of 50% cytotoxic-T cells and 50% tumor cells compared to a theoretical sample of pure tumors, based on single cell RNA-seq data (see methods and results) is plotted on the Y-axis (top and bottom panels). The actual observed ratio of group geometric means from tumors in cluster 1 compared to cluster 2 (top panel) or clusters 3–7 (bottom panel) for all 118 OXPHOG genes was plotted on the X-axis. Ratios for genes with symbols beneath the identity function (dotted line) in quadrants II and IV, or above the identity function in quadrants I and III are highly unlikely to be explained by increased cytotoxic T-cells in cluster 1. Yellow zones in the plot are regions where contaminating T-cells could possibly contribute to differences in gene expression found for patient cluster 1. Blue symbols represent genes that were significantly different in cluster 1 compared to other clusters, and black symbols represent no significant differences in gene expression levels. Circles correspond to genes that function in oxidative phosphorylation, and square symbols represent genes that regulate glycolysis.