Extended Data Fig. 9: Pathway enrichment analysis in spatial transcriptomics and IMC datasets.

a, Enrichment scores for hallmark pathways in MsigDB across all ROIs in the GeoMx dataset. b–e, Enrichment score of selected pathways from a, across disease groups but dependent on the location within the lung from which they were obtained. **P < 0.01; *P < 0.05, two-sided Mann–Whitney U-test, pairwise between groups, Benjamini–Hochberg FDR adjustment. f, g, Pairwise Pearson correlation of cell-type abundances between IMC samples (f) or disease groups (g). h–j, UMAP (h), diffusion map (i) or PCA (j) projection of IMC images, coloured by disease group, subgroup or sample identifier.