Extended Data Fig. 6: Progesterone induced genes are down-regulated post-UA treatment.

A) UpSet plot depicting up-regulated genes (>0.25 log FC, pval <0.05 - Memento analysis) post-UA treatment across all 7 broad cell types. Intersection size indicates the number of genes that are uniquely regulated within a single cell type or shared across two or more cell types. B) Pathway analysis of LHS cells comparing post-treatment to baseline. Intersection size indicates the number of genes within each pathway gene set. Fisher’s one-tailed test p-values were corrected using Benjamini-Hochberg FDR, with adjusted p-value < 0.05 threshold for presented pathways. C) Dot plot (upper) and summary boxplots (lower) for TNFSF11 and CXCL13 gene expression across participant samples at baseline (B) and post-treatment (PT). Cell fraction represents the percentage of cells within LHS cells expressing each gene with mean expression overlaid (upper) or plotted on the y-axis (lower). Box plots centre lines represent median values, box bounds indicate the 25th and 75th percentiles, and whiskers extend to the most extreme datapoint within 1.5 × IQR (inter-quartile range) of the outer hinge of the boxplot. P-value and log fold change (post-treatment/baseline) determined using Memento are overlaid. Memento significance is calculated using a nonparametric permutation test where observed mean differences are compared to a null distribution generated by permuting treatment group labels. N = 6 tissue pairs. D) UpSet plot depicting up-regulated genes that encode proteins that act as ligands (>0.25 log FC, pval <0.05 - Memento analysis) post-UA treatment across all 7 broad cell types.