Fig. 6

Intercellular communication networks among tissues. a-c The top 10 significant ligand-receptor interactions between cells among different organs for epithelial and myeloid cell subtypes (a), myeloid and CD8⁺ T cell subtypes (b), and CD8⁺ T and stromal cell subtypes (c; fibroblast, smooth muscle cell, and FibSmo cell). An interaction is indicated as color-filled circle at the cross of interacting cell types in a tissue (x-axis) and a ligand-receptor pair (y-axis), with circle size representing the significance of −log₁₀P values in a permutation test and colors representing the means of the average expression level of the interacting pair. The naming system is as follows: taking an example of “EGFR_TGFB1” in “cholang_FXYD2.Mac.Commonbileduct,” the ligand-receptor pair is EGFR (red) and TGFB1 (black), and the circle is colored based on the expression levels of EGFR in cholang_FXYD2 cluster and TFGB1 in Mac cluster in the tissue Commonbileduct. Mon, monocyte; Mac, macrophage; DC, dendritic cell; TRM, tissue-resident memory T cell; TEFF, effector T cell; TGD, γδ T cell; MAIT, mucosal-associated invariant T cell; TEM, effector memory T cell; TIEL, intraepithelial T lymphocyte; TN, naïve T cell; Fib, fibroblast; Smo, smooth muscle cell; FibSmo, novel cell type named FibSmo cell; Commonbileduct, common bile duct; Lymphnode, lymph node; Smallintestine, small intestine. For epithelial cells, the full names of each cluster refer to Table S47. d Connection graph showing the intensity of interactions between one organ to another in colored circles. Interactions were evaluated between major cell types including CD4⁺ T cell, CD8⁺ T cell, γδ T cell, B cell, plasma cell, myeloid cell, NK cell, epithelial cell, fibroblast, smooth muscle cell, FibSmo cell, and endothelial cell. Numbers in red show the total counts of ligand-receptor pairs between the indicated organ and all others, which include only the unique significant interacting pairs between them (average expression > 0 and P value < 0.05). e Connection graph showing the intensity of interactions within a major cell type or between two major cell types in colored circles. Numbers in red show the total counts of ligand-receptor pairs within or between cell types, which only included the unique significant interacting pairs between them (average expression > 0 and P value < 0.05). CD4, CD4⁺ T cell; CD8, CD8⁺ T cell; γδ, γδ T cell; B, B cell; Plasma, plasma cell; Myeloid, myeloid cell; NK, NK cell; Epi, epithelial cell; Fib, fibroblast; Smo, smooth muscle cell; FibSmo, FibSmo cell; Endo, endothelial cell