Ligand–receptor analysis to assess endothelial and tip cell interactions with other cell types after SCI. (A) Overview of ligand–receptor analysis method. Interaction scores were calculated as the mean of the average log-normalized expression of receptor gene in one cell type and the average log-normalized expression of ligand gene in a second cell type. To test for enrichment in specific pairs, we used a permutation test and compared scores against these random values (see Materials and methods). (B) Dot plot of the interaction scores at 1 dpi between select myeloid subtypes as the ligand-expressing cell (top axis) and endothelial/tip cells as the receptor-expressing cells (bottom axis). Specific ligand–receptor pairs are listed along left axis. Size of the dot indicates –log₁₀(P value). Color of dot indicates interaction score where dark red dots signify stronger predicted interactions. (C) Dot plot of the interaction scores at 1 dpi between vascular subtypes and endothelial/tip cells. (D) Dot plot of interaction scores at 1 dpi between select macroglial subtypes (see Fig. 8) and endothelial/tip cells. (E) Dot plot of expression of Angpts (left of dotted line) and their receptors (right of dotted line) in cell types across all time points. (F) Dot plot of expression of VEGF family member ligands (left of dotted line) and their receptors (right of dotted line) in cell types across all time points. In E and F, color of dots indicates z-scored expression, and size of dot indicates percentage of cells with at least one UMI detected per gene. Inset stars indicate statistically significant greater expression compared with all other cells combined (adjusted P value < 10⁻¹⁰; Wilcoxon rank-sum with Bonferroni correction; see Materials and methods). Div, dividing; Oligo, oligodendrocyte; OPC, oligodendrocyte progenitor cell; VSMC, vascular smooth muscle cell.