Fig. 5: Stratification of MSI and MSS CRC patients based on scRNA-seq signaling modules.

a, b Visual representation of single cell patient subgroup detection. CD8⁺ T cell population counts per patient are shown as relative proportions (stacked bar plots). For each patient, the ratio of bystander activation signature expression to TCR activation expression is represented as a dot at the basis of an arrow (Supplementary Table S3). Arrows indicated the difference in median correlation between TCR activation and bystander activation when compared to the corresponding resting state. Dot plots on the right-hand side indicated the number of cells positive for expression of important immune-inhibitory receptor (IR) genes when compared to a threshold value. Vertical lines “|” in gene names indicate double positive cells for the genes indicated. The size of the dots represents the proportion of this population compared to the total CD8⁺ T cell pool. Heatmaps represent the expression of the tumor-reactive signaling modules. a MSI CRC patients were stratified into roughly two tumor-associated clusters (indicated on the right-hand side with a number, containing six patients for group 1 and 16 for group 2) using hierarchical clustering on the tumor-reactive signaling module scores (central heatmap). b MSS CRC patients were roughly stratified into three tumor-associated clusters using hierarchical clustering on the expression of the tumor-reactive signaling modules (heatmap), as indicated on the right-hand side with a number; 1: 14 patients, 2: 10 patients, 3: 14 patients. Data for three patients was not available due to thresholding.