Fig. 2: The chromatin landscape of dysfunctional T cells.
From: A single-cell map of dynamic chromatin landscapes of immune cells in renal cell carcinoma
a, Violin plots of gene activity scores of the indicated genes for effector/nondysfunctional (C4,5,7_CD8) and dysfunctional (C8,9,10,11_CD8) T cell clusters. Pairwise comparisons of gene activity scores for the indicated gene between specified T cell clusters were determined using a two-sided Wilcoxon rank-sum test. The P values obtained were subjected to multi-test correction with the FDR method (****adjusted P < 0.0001; raw adjusted P values are listed in the source data; for clusters 4, 5, 7, 8, 9, 10, 11, n = 1,810, 1,821, 873, 924, 1,775, 2,440 and 1,613 cells, respectively). b, Cell alignment to the pseudotime developmental trajectory within the dysfunctional CD8+ T cell populations. The smoothened arrow represents a visualization of the interpreted trajectory in the UMAP embedding. c, Pseudotime heatmap ordering of gene activity scores of the top 10% most variable genes across the potential CD8+ T cell dysfunction trajectory. General ordering of cells from different dysfunction clusters along the pseudotime course is marked along the trajectory at the top. d, Pseudotime heatmap ordering of the top 10% most variable chromVAR TF motif bias-corrected deviations in the CD8+ T cell dysfunction trajectory (for b, c and d, n = 6,752 cells).
