Extended Data Fig. 4: Carotid plaque EC subcellular genes and related biological processes.
a) Volcano plots showing differentially expressed EC2 genes (red, up-regulated; blue, down-regulated) using all other EC subclusters 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 EC2 subcluster genes overlapping with the GO category. b) Volcano plots showing differentially expressed EC4 genes (red, up-regulated; blue, down-regulated) using all other EC subclusters 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 EC4 subcluster genes overlapping with the GO category.
