Fig. 2: Stromal features associated with high- and low-stromal TIME.

a Average expression of selected cytokines and surface proteins (SPs) in each cell type and tumor group. Dot plot showing the mean gene expression z-score of differentially expressed cytokines and SPs across cell types. The expression of each gene is normalized to a mean value of zero and unit standard deviation. Expression values are indicated by color. Adjusted p-values for each differentially expressed gene between high- and low-groups are indicated by circle size. Statistical significance is coded by the following symbols. p-value < 0.1, *p-value < 0.05, **p-value < 0.01, and ***p-value < 0.001. b Heatmap revealing correlations between inferred TF activities (columns) and SP/cytokine expression (rows) in CA-MSCs, fibroblasts, and myofibroblasts. For clarity, we selected highly correlated SP/cytokine-TF pairs (Table S4) and used the union of the selected genes. The correlation coefficients of the top correlated TFs with each SP/cytokine are shown for each cell type. c, d Scatter plots of selected highly correlated gene-TF pairs for each cell type. Each dot represents a cell colored by the tumor group.