Extended Data Fig. 7: Pathway enrichment and target gene analysis for the SMI data.

a, Ligand–receptor (LR) interactions significantly up- or down- regulated in treated samples between CAF and malignant cells, related to Fig. 5a. The cost functions used were Eq. 6 (left) and 7 (right) (Methods). Benjamini-Hochberg corrected two-sided Mann-Whitney U tests. b, Differentially enriched LR interactions inferred with a mixed effects model test (two-sided, Benjamini-Hochberg adjusted p value, Methods). c, Comparison of ligand and receptor gene expression between SCOTIA-inferred interactions versus non-interacting CAF–malignant cell pairs. Two-sided Mann-Whitney U tests (CLCF1–CNTFR: untreated, n = 158; treated: n = 89. WNT5A–FZD5: untreated, n = 170; treated: n = 98). d, Pathway enrichment analysis with ligand (left) or receptor (right) gene sets from Fig. 5b. Top pathways enriched in untreated (purple) and treated (red) tumors are shown. Benjamini-Hochberg corrected one-sided Fisher’s exact test. e, Boxplots summarizing the difference in target gene expression between significantly up- and down-regulated LR groups for five other abundant cell type pairs. Two-sided Mann-Whitney U test. Malignant–CAF, up: n = 82; down: n = 6. Malignant–macrophage, up: n = 30; down: n = 3. CAF–macrophage, up: n = 20; down: n = 19. Macrophage–CAF, up: n = 56; down: n = 29. Macrophage–malignant, up: n = 10; down: n = 3. For boxplots in panel c and e, the box limits denote the first and third quartiles, with the median shown in the center and whiskers covering data within 1.5× the interquartile range from the box, with diamonds representing outliers.