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- Ovarian cancer mutational processes drive site-specific immune evasion

Site specificity of immunophenotypes
a, UMAP plot of T and NK cell clusters profiled by scRNA-seq. Clusters are coloured and numbered to reference cluster labels in c. b, Pairwise comparisons of kernel density estimates in UMAP space. c, Left, heatmap of average T cell state module scores (left) and signalling pathway activity scores (right) across CD4⁺ T, CD8⁺ T, innate lymphoid cell (ILC), NK and cycling cell clusters. Right, dot plot showing site-specific enrichment of T and NK cell clusters based on GLM. The colour gradient indicates the log2-transformed odds ratio (red, enrichment; blue, depletion), and sizes indicate the Bonferroni-corrected –log10(P value). d, Intra-sample diversity of T and NK cell clusters estimated by Shannon entropy with samples grouped by site (patient and sample counts shown) and intra- and inter-patient dissimilarity of T and NK cell cluster composition for pairs of samples, estimated using the Bray–Curtis distance (patient and sample pair counts shown). Pairwise dissimilarity is shown for all heterotypic pairs of sites (adnexa versus non-adnexa, adnexa versus ascites, non-adnexa versus ascites). Violin plots show the median, top and bottom quartiles; whiskers correspond to 1.5× IQR. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. e, Top, diffusion maps of the subset of CD8⁺ T cells profiled by scRNA-seq, with cells coloured by CD8⁺ T cell cluster and pseudotime. Bottom, relative expression of genes marking CD8⁺ T cell clusters in diffusion space. DC, diffusion component. f, Scaled module scores with respect to pseudotime.
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