Fig. 5

The heterogeneity of epithelial cells inter- and intra-organ tissues. a t-SNE plots of 17,436 epithelial cells. Each dot represents one cell, colored according to their origins of tissues (top panel) or cell clusters (bottom panel). b Dot plot visualizing the normalized expression of marker genes for each epithelial cluster. Cell cluster at y-axis was coded in numbers on the left, corresponding to that in a. Marker genes are shown at the x-axis. The size of the dot represents the percentage of cells with a cell type, and the color represents the average expression level. c Dendrogram of 34 clusters based on their normalized mean expression values (correlation distance metric, complete linkage). Only genes with fold change above 1.5, p.adjust < 0.05, and pct.1 ≥ 0.2 in each cluster were included in the analysis. d Volcano plot shows the DEGs between the 14 digestive and 20 non-digestive related clusters. Labeled genes are markers for each cluster in b. e, f Gene Ontology enrichment analysis results of each epithelial cell cluster in the digestive organs (e) and non-digestive organs (f). Cell clusters in columns are coded as numbers at the bottom, correspond to that in a, and are colored according to their −log₁₀P values, with white to red for low to high enrichment of a GO term in a row indicated on the right. Only the top 20 significant GO terms (P value < 0.05) are shown. g Heat map of the activation scores of epithelial cell subtypes for gene expression regulated by transcription factors (TFs). Cell clusters are indicated on top, and the scores were estimated using SCENIC analysis. Only the top 10 TFs are shown with the highest difference in expression regulation estimates between each cluster and all other cells, tested with a Wilcoxon rank-sum test. The cluster numbers are in reference to those in a. Cell clusters are grouped according to the origin of organ and their digestive or non-digestive function as indicated on top