Fig. 6: Heterogeneity of endothelial cells.
a, UMAP visualization displaying the distribution of endothelial MetaCells, colored by cell type; venEndo, venous endothelial; lymEndo, lymphatic endothelial. b, Box plot depicting the ECM signature score for each endothelial cell type, calculated from 367 samples. The bottom of the box represents Q1, and the top of the box represents Q3. The height of the box represents the IQR, whereas the horizontal line inside the box indicates the median. The whiskers extend to the positions of Q1 – 1.5 × IQR and Q3 + 1.5 × IQR. c, Violin plot showing the expression of representative marker genes for each endothelial cell type. d, Scatter plot illustrating the antigen-presenting and tip signature scores of endothelial subsets. e, Box plot showing the proportions of distinct endothelial cell types in various sample categories, including normal tissue (green), precancerous tissue (orange), tumor tissue (purple) and metastatic tissue (blue), derived from 344 treatment-naive samples. Significance labels in the figure were assessed via Kruskal–Wallis tests to compare each subset distribution among four tissue types. Significance for pairwise source proportions within each cell type, assessed via two-tailed unpaired Wilcoxon tests, is reported in Supplementary Table 6. The open rectangle annotates the comparative scope, with BH correction for multiple testing. The bottom of the box represents Q1, and the top of the box represents Q3. The height of the box represents the IQR, whereas the horizontal line inside the box indicates the median. The whiskers extend to the positions of Q1 – 1.5 × IQR and Q3 + 1.5 × IQR. f, Heat map showing the proportion of different endothelial cell types in cancer types and healthy tissues. For rows, a bar plot to the left of each row illustrates the number of MetaCells (in log10 scale) and origin of cancer cells, color-coded for clarity. g, Genes encoding the top 20 ligands inferred to regulate RGCC+ endothelial cells according to NicheNet. Ligands are ranked by Pearson correlation (left), and a dot plot represents the expression percentage (dot size) and value (dot intensity) of the top 20 ligands.