Fig. 4

Potential causes of inter-tumor immune infiltration heterogeneity. a In selected cancer types, counts of total somatic coding mutations positively associated with the level of infiltrating immune cells. The y-axis is the residual of corresponding immune cell abundance after linear regression against tumor purity. Statistical significance was evaluated using partial Spearman’s correlation adjusted for tumor purity. The asterisk indicates only HPV-negative tumors were selected for head and neck cancer. Multiple test correction was performed across cancer types and six immune components. Gray hues indicate previously known results (HNSC, LGG, and LUSC), while other findings are novel in this study. b CD8 T-cell infiltration is associated with microsatellite instability (MSI) status in cancers commonly with MSI. MSI-H high level of microsatellite instability, MSI-L low level of microsatellite instability; MSS microsatellite stable. Statistical significance was evaluated using a Wilcoxon rank sum test. c, d Chemokine/receptor networks for immune infiltration in diverse cancer types. Vertexes are ligands (green) and receptors (purple) and edges indicate known molecular interactions. For each cancer, the partial correlations (corrected for purity) between the chemokine gene expression and infiltration of CD8 T cells (c) or macrophages (d) were calculated. For a pair of interacting chemokine and receptor genes, if both are significantly correlated with immune cell infiltration in one cancer, a colored dot represents the cancer type is placed on the edge connecting the chemokine and receptor. Statistical significance was evaluated using partial Spearman’s correlation at a false discovery rate threshold of 0.01. Heatmap visualizations of the same results are shown in Additional file 1: Figure S6c, d