Fig. 2.

Gene expression traits and methylation patterns associated with West African ancestry in hepatocytes. a Enhanced volcano plot of gene expression traits associated with increasing WAA plotted against −log₁₀ p values of all 18,854 genes expressed in hepatocytes and 131 genes significantly associated with WAA represented as red and blue circles (red circles: FDR < 0.05 and logFC > 1.5 and <−1.5; blue circles: FDR < 0.05 and logFC < 1.5 and >−1.5; green circles: FDR > 0.05 and logFC > 1.5 and <−1.5, gray circles: FDR > 0.05 and logFC < 1.5 and >−1.5) and b enhanced volcano plot of gene expression traits associated with increasing WAA plotted against −log₁₀ p values within the subset of 64 PharmGKB “very important genes” (red circles: p < 0.05 and logFC > 1.0; blue circles: p value < 0.05 and logFC < 1.0; gray circles: p value > 0.05). c Correlation of 1034 unique genes containing DMRs significantly associated with WAA (mean Beta fold change from DMRcate) with coefficient of gene expression at each gene (indicating the direction of association to ancestry). Each point represents a gene, with gray triangles representing hypomethylated genes (Pearson’s r = −0.014, p = 0.009) and maroon red circles representing hypermethylated genes (Pearson’s r = 0.036, p = 0.55). Gray and maroon hash marks on the x- and y-axis represent genes plotted with both expression and methylation values. Gray and maroon shading around each regression line represents the C.I. 95%. d Q–Q plot of the observed versus expected −log₁₀ p values in the replication cohort (n = 206). Each point represents a gene with the colored lines representing different FDR thresholds of significance