Fig. 4

Replicated genes and replicated DARs. a, b Schematic representation of two levels of replication between the PW and NBB cohorts. H3K27ac peaks are illustrated by colored lines, representing control (blue) and PD (orange) samples, with the height of the peak representing the peak intensity. Shown is a hypothetical gene X, with exons represented as grey boxes and introns represented by lines. In both cases, the gene has two pairs of common peaks: Peak_a/A, mapped to the first exon of the gene and Peak_b/B, mapped to the third exon of the gene. a Altered H3K27 acetylation occurs at different regions of gene X in each cohort. Thus, while gene X harbors altered H3K27 acetylation in both cohorts (i.e. gene X is a replicated gene), it does not harbor replicated DARs. b Altered H3K27 acetylation occurs at the same region of gene X in both cohorts. In this case, gene X is a replicated gene with a replicated DAR. c Venn diagram showing the number of replicated genes (with or without replicated DARs) between the two cohorts, out of all genes represented in our ChIP-seq data from both cohorts. d Venn diagrams showing the number of replicated DARs between the two cohorts, out of all common peak pairs (left) and their corresponding annotated genes (right). e Venn diagram showing the overlap of PD-implicated genes with DARs between cohorts. All DARs exhibited hyperacetylation. f Venn diagram showing the number of PD-implicated genes with adjusted metaP < 0.05