Fig. 2. Cell-specific OCRs, overlap with DNAse-seq, and biological functions.

a Examples of genes with cell-specific open chromatin. Cell types from top to bottom are; glutamatergic neurons, GABAergic neurons, oligodendrocytes, and microglia/astrocytes. b Overlap between cell-specific open chromatin (ATAC-seq) and 127 samples from REMC (DNase-seq). The overlap was calculated by the Jaccard index of the base pair overlap. Samples from REMC were aggregated into four groups: brain tissue, brain-derived cells, immune cells/tissues, and other non-brain cells/tissues. The center shows the median, the box shows the interquartile range, whiskers indicate the highest/lowest values within 1.5x the interquartile range, and outliers from this are shown as dots. The number of independent sample overlaps represented by the boxplot groups are as follows: Brain tissue: 10, Brain cells: 6, Immune: 30, and Other: 81. To assess the significance of the differences in overlap for our cell-specific OCRs with the four REMC categories, a multiple regression analysis with the “Other” category as the intercept was done. P-values indicate significance of enrichment/depletion against the other category uncorrected for multiple testing. c Overlap between cell-specific open chromatin (ATAC-seq) and gene sets representing biological processes and pathways. Only those that were within the top ten most significant gene sets in one or more ATAC-seq categories are shown. Pathways were clustered by the Jaccard index using the WardD method. “#”: one-sided binomial FDR < 0.001, “·”: one-sided binomial FDR < 0.05, “Bi”: BIOCARTA, “GO”: gene ontology, “KG”: KEGG, “Re”: REACTOME, “Reg.”: regulation, “Pos.” positive, “Neg.” negative.