Fig. 4: Single-cell RNA sequence characterization of EC subcellular clusters in carotid plaques of female and male patients.
a, Subcellular clusters of human carotid plaque ECs visualized with UMAP. vv, vasa vasorum; cl, carotid lumen. The inserted violin plots show the EC subcluster expression levels of the capillary EC marker, SPARCL1, and the luminal EC marker, VWF. b, Dot plot showing the expression levels of functional gene markers within the five EC subclusters. c, UMAPs of EC subcellular clusters highlighted for cells isolated from carotid plaques of female and male patients. d, Bar plots showing the relative sex specificity of cells in each EC subcluster. The total number of cells collected in each category are shown in parentheses. P values were calculated using chi-square statistics assessing the statistical significance between observed and expected values. e, Volcano plots showing differentially expressed EC1 genes (red, upregulated; blue, downregulated) using all other EC subcluster as background. Cell-type-specific gene enrichment was calculated using Wilcoxon rank-sum test (log2(fold) > 0.3, Bonferroni-adjusted P < 0.005). Dot plots show top-ranked biological processes according to GO. Gene ratios (x axis) are the relative number of subcluster genes in relation to the total gene count in each GO category. Dot size indicates the actual number of subcluster genes in each GO category. GO enrichment −log10(P values) were calculated with Fisher exact test. Cluster genes indicate the number of EC1 subcluster genes overlapping with the GO category. GPCR, G protein-coupled receptor; RPTK, receptor protein tyrosine kinase; BBB, blood–brain barrier.
