Fig. 6: Cell-cell interactions between epithelial cells and other cell types.
a The interactions between epithelial cells (LE_0, LE_5, Gland_10 and prolifEpi_20) and three stromal cells (Str_2, Str_3 and Str_11). The most left represents ligands of epithelium defined by NicheNet Pearson correlation and they are ranged by the ability of each ligand to their targets. The dot plots indicate their different expression of ligands in epithelial cells and predicted targets in stromal cells. Heatmap represents the predicted ligands activity by NicheNet on their target genes in stromal cells. Yellow color bar represents the Pearson correlation coefficient, purple color bar represents regulatory potential and magenta color bar represents nomalized expression of genes. b Heatmap represents the interactions between ligands in epithelial cells (LE_0, LE_5, Gland_10 and prolifEpi_20) and their receptors in stromal cells (Str_2, Str_3 and Str_11). Dot plots represent the average expression levels of ligands and receptors in epithelial and stromal cells, respectively. Color bar in the bottom left corner represents nomalized expression of genes, color bar in the top right corner represents interaction potential. c–e UMAP visualization of the expression of Ifne, Ifnra1 and Ifnra2 in days 16 and 19 mice. Color bar represents expression of indicated gene in cells. f The interactions between epithelial cells (LE_0, LE_5, Gland_10, and prolifEpi_20) and macrophages (Mac_4, Mac_9, and Mono_14). The most left represents ligands of epithelium defined by NicheNet Pearson correlation and they are ranged by the ability of each ligand to their target. The dot plots indicate their different expression of ligands in epithelial cells and predicted targets in macrophages and monocytes. Heatmap represents the predicted ligands activity by NicheNet on their target genes in macrophages. Yellow color bar represents the Pearson correlation coefficient, purple color bar represents regulatory potential and magenta color bar represents nomalized expression of genes. g Heatmap represents the real interactions between ligands in epithelial cells (LE_0, LE_5, Gland_10 and prolifEpi_20) and targets in macrophages (Mac_4, Mac_9 and Mono_14). Dot plots represent the average expression levels of ligands and receptors in epithelial and macrophages and monocytes, respectively. Color bar in the bottom left corner represents nomalized expression of genes, color bar in the top right corner represents interaction potential. h UMAP visualization of the expression of Csf3 in days 16 and 19 epithelium. Color bar represents expression of indicated gene in cells. i The changed ligand-receptor pairs between different cell types in Shp2f/f and Shp2d/d mice determined by CellphoneDB. The size of dot: the expression of ligands (pink) and receptors (blue) in different cell types, color bar: the significance of enriching. The numbers of colored round representing different cell types. P values are derived from one-sided permutation tests based on statistical framework in CellphoneDB. Color bar represents pValue of ligand receptor.
