Extended Data Fig. 9: Cell type identification through multiplex immunohistochemistry (MILAN).
a, Dotplot showing expression of cell type markers across final annotated cell types. b, Boxplots showing number of interactions of pre-exhausted CD8+ T cells with other cell types. N numbers indicate independent cells per HLApr/ICB-response group. Effect size metric was calculated as Cohen’s D (positive values indicating higher in HLAprLOW/ICB-responders) and two-sided p-values shown are extracted through Kolmogorov-Smirnov tests (multiple testing corrected with false discovery rate with Benjamini-Hochberg method). c, Boxplots showing number of interactions of exhausted CD8+ T cells with other cell types. N numbers indicate independent cells per HLApr/ICB-response group. Effect size metric is shown by Cohen’s D (positive values indicating higher in HLAprLOW/ICB-responders) and two-sided p-values shown are extracted through Kolmogorov-Smirnov tests (multiple testing corrected with false discovery rate). For all boxplots in this figure, boxes represent median (centre) and first/third quartile (bottom and top, resp.) values; whiskers show most extreme values within 1,5x interquartile range (IQR). Outliers extending beyond 1.5x IQR above/below the median were omitted from visualisation.
