Fig. 3: Expression profile and development of Treg cells.

a Violin plots showed the IL2R (left panel), inhibitory (middle panel), and co-stimulatory (right panel) scores for each Treg cell cluster (n = 11,631). Box plots inside the violins indicated the quartiles of corresponding score levels. Endpoints depict minimum and maximum values; centre lines denote median values; whiskers denote 1.5× the interquartile range; black dots denote each cell. Violin plots are coloured according to cell types, and signature scores are indicated at the y-axis. b Heatmap showed the selected signalling pathways (rows) that were significantly enriched in GO and KEGG analyses for each Treg cell cluster (columns). Filled colours from blue to red represent scaled expression levels (normalised −log₁₀P values) from low to high. P values were calculated by one-sided hypergeometric test and adjusted for multiple comparisons. Orange and purple squares on the left column represent the results derived from GO and KEGG signalling pathways analysis, respectively. c Pseudotime trajectory analysis of Treg cells (Treg_C1, Treg_C2, Treg_C3, and Treg_C4; n = 11,631) with high variable genes. Each dot represents one single cell, coloured according to its cluster label. The inlet plot showed each cell with a pseudotime score from dark blue to yellow, indicating early and terminal states, respectively. d Box plots showed the expansion- (top panel) and migration-index (bottom panel) scores of each CD4⁺ T cell cluster (n = 10). Comparison was made using two-sided Wilcoxon test. Cell clusters are indicated at the x-axis, and the y-axis shows the expansion- or migration-index at the top or bottom panel, respectively. Endpoints depict minimum and maximum values; centre lines denote median values; whiskers denote 1.5× the interquartile range; coloured dots denote each patient. e Box plots showed the transition-index scores of Treg_C4_TNFRSF4 (left panel) and Treg_C2_HSPA1A (right panel) with other Treg cells (n = 10). Comparison was made using two-sided Kruskal-Wallis test. Cell clusters and the transition-index scores are indicated at the x- and y-axis, respectively. Endpoints depict minimum and maximum values; centre lines denote median values; whiskers denote 1.5× the interquartile range; coloured dots denote each patient.