Fig. 2
Alterations in DNA methylation at cg10696062 in WNT5B are associated with AD neuropathology in the EC. a A Manhattan plot of association between DNA methylation (purple, above X-axis) and DNA hydroxymethylation (yellow, below X-axis) with Braak stage in the EC highlights associations at loci across the genome. One DMP in WNT5B (cg10696062) was experiment-wide significant (P < 2.4 × 10− 7). With increasing Braak stage cg10696062 showed an experiment-wide significant increase in 5mC (P = 1.47 × 10−7), in parallel with a nominally significant decrease in 5hmC (P = 1.56 × 10−4) and uC (P = 0.02). b Scatter plot of residual values, corrected for age, sex, and neuron/glia proportion, against Braak stage for cg10696062 with purple circles representing 5mC levels, yellow circles representing 5hmC levels, and gray circles representing uC levels. Regression lines are shown for 5mC (purple line), 5hmC (yellow line), and uC levels (gray line). c Stack chart depicting differences in adjusted beta value (controlling for age, sex, and neuron/glia proportion) between individuals with low (Braak Stage 0–II) and high (Braak Stage V–VI) pathology for 5mC (purple), 5hmC (yellow), and uC (gray) levels