Fig. 2

T cell clusters. a tSNE plots of 12,941 T cells, color by relevant clusters (top) or sample type (bottom). b Color coding for expression (gray to blue) of marker genes of natural killer cells, CD8 + T cells, CD4 + T cells, regulatory T cells and TOP2A + cells. c Differences in pathway activity of each cell scored by GSVA between T cells isolated from normal, interface and tumor zone zones. d As in c, but for CD4 + T cells (clusters 1, 2 and 8), CD8 + T cells (clusters 0, 4, 5 and 7) and regulatory T cells (clusters 3 and 6). e Violin plots displaying the expression of selected genes encoding granzyme (GZMA, GZMM and GZMK) and immune checkpoint (CTLA4 and TIGIT) in T cell clusters. f Overall survival curves of breast cancer patients stratified by the average expression of top 10 marker genes of regulatory T cell clusters. Binary: high versus low, n = 535 or 535 patients, respectively. Expression threshold set to median to split the high-expression and low-expression cohorts. g Heatmap of single-cell regulon scores inferred by SCENIC. Number in brackets is the number of the target genes. g, genes