Fig. 5: Characterization of the demyelination-affected endothelial subpopulation (LPC1) identified by HiDDEN.

a Dotplot of mean expression at 3 dpi of LPC1 marker genes ordered by p-value. P-values are calculated using a one-sided Wilcoxon rank sum test with Benjamini-Hochberg correction. b Validation of gene expression with fluorescent in-situ hybridization (FISH) and confocal microscopy showing presence of endothelial cells (Flt1-positive cells, green) coexpressing Lgals1 (red) and S100a6 (magenta) specifically present in demyelinating lesion (top) and not control (bottom) brains, 3 days after injection. Left: Overview of a demyelinating or control white matter lesion. Corpus callosum outlined in gray dashed line. Right: High-resolution confocal images of single endothelial cells. All images are representative of n = 2–3. Scale bars are left top = 200um, left bottom = 100um, right = 10um. c Significantly enriched GO molecular function terms (top) and Reactome pathways (bottom) based on LPC1 marker genes ordered by significance. The reported p-values are computed using the over-representation statistical test in g:Profiler and are Bonferroni-adjusted. d ReviGO plot summarizing the significantly enriched GO biological processes based on LPC1 marker genes colored by significance with selected labels. Significance values are computed in the same was as described in c. Dot size indicates the log10 of the number of genes associated with each term. e Significantly enriched (purple) and depleted (green) ligand-receptor interactions between LPC1 (relative to LPC0) endothelial cells and neighboring cell types split by interaction direction: from endothelial to neighboring cell type (left), and from neighboring cell type to endothelial (right). P values are calculated using a one-sided permutation test. f Dot plots of mean expression of Vcam1 across time and condition labels. Source data of (a, c, d, e, f) are provided as a Source Data file.