Extended Data Fig. 5: enhancer-gene link.
From: Population-level variation in enhancer expression identifies disease mechanisms in the human brain
a, the expression level of different classes of genes and enhancers (Nintergeric_enhancer = 4,626, Nintronic_enhancer = 37,358, NlincRNA = 2,915, Nprotein_coding_gene = 16,468). Box plot indicates median, interquartile range (IQR), and 1.5 × IQR. b, Pairwise Spearman correlation coefficient (SCC) between samples of different classes of genes/enhancers of discovery vs discovery (DD), discovery vs replicate (DR), and replicate vs replicate (RR) (Nintergeric_enhancer = 4,080, Nintronic_enhancer = 36,493, NlincRNA = 2,665, Nprotein_coding_gene = 16,175). Box plots as in a. c, Distribution of gene FPKM (fragments per kilobase of transcript per million mapped reads) and counts for linked enhancers. Linked genes have a significantly higher gene expression (FPKM, two-sided Wilcoxon test, P < 10−16). Box plots as in a. d, Distribution of enhancer CPM and for counts linked genes. Linked enhancers do not have a higher expression (CPM, two-sided Wilcoxon test, P = 0.96). Box plots as in a. e, Distance between enhancers to genes of linked group and background (Nlink = 35,964, Nbackground = 241,040). f, Distance between enhancers to genes of linked group and background, physically-overlapped gene-enhancer pairs were excluded (Nlink = 22,920, Nbackground = 220,062). Box plots as in a. g, Neuronal vs non-neuronal t statistics for linked and non-linked enhancers. Linked enhancer has a significantly higher value (two-sided KS test, P < 10−16).
