Extended Data Fig. 4: Combined analysis of ER⁺/FOXA1⁻/GATA3⁻ cells, duct/lobule-adjusted phenotypes, and NK/T cell composition.

a, Identification of HR⁺ (FOXA1⁺/GATA3⁺/ER⁺/PR⁺/AR⁺) and ER⁺ only populations. b, Effect sizes for associations between HR-populations and epithelial phenotype presence (p-values from two-sided paired Wilcoxon signed-rank tests) with right-side boxplots showing HR phenotype proportions. c, Relationship between HR-population proportion of epithelial compartment and age (two-sided Spearman rank correlation coefficient tests performed). d, Boxplots comparing proliferative fraction, cell area, and axis ratio between HR⁺ and ER⁺ cells (paired Wilcoxon tests). e, Boxplots of duct vs. lobule assignment of HR⁺ and ER⁺ populations; p-values are from paired Wilcoxon tests from patients with both ductal and lobular cells. f, Odds ratios for epithelial phenotype proportions based on an age cutoff of 50, adjusted for duct/lobule epithelial cell proportions in each image (unadjusted and adjusted estimates shown, 95% CIs, p-values from two-sided binomial generalised linear mixed-effects models with Benjamini-Hochberg correction). g, As in f, for microenvironment phenotypes. h, Bar plots of cells expressing CD45 and/or CD56. i, Relationship between NK cell density and age, as in c. j, Bar plots of TCF1, PD-1, and GZMB status for CD4⁺T and CD8⁺T phenotypes. k, Effect sizes for associations between marker positivity of the CD4⁺T or CD8⁺T compartment and age (two sided Mann-Whitney U tests, BH-corrected, with right-side boxplots of compartment proportions). For all effect size plots, circles represent point estimates corresponding to median differences between groups, and whiskers indicate 95% confidence intervals with p-values corrected for multiple testing with the BH method. For all scatterplots, correlation coefficients (ρ) and p-values are derived from Spearman rank correlation coefficient tests; loess regression lines are shown. For all boxplots, boxes show 25th, 50th, and 75th centiles; whiskers indicate 25th/75th centiles ± 1.5 × interquartile range; points beyond whiskers are outliers.