Fig. 3: Large clusters of D1/D2 5mC differences and more scattered 5hmC differences.
a Manhattan plots of 5mC and 5hmC differences along the autosomes. Dots represent 1-kb windows. The P value is plotted upwards when the modification is enriched in D1 vs. D2 neurons, and downwards otherwise. Circled numbers represent the biggest clusters of windows, numbered from left to right, which are referred to in the text and in other panels of this figure. P, adjusted P value. b Venn diagrams of the significant 1-kb windows. c Clustering of the significant 1-kb windows. The pie charts show the proportions of 1-kb windows that are in a cluster (as defined in Methods). d Distribution of the cluster sizes for 5mC and 5hmC. Clusters are ordered from the largest to the smallest. e Genome browser representation of the differentially methylated cluster number 10 (as numbered in panel (a)). f Hi–C interaction frequencies from the study of Bonev et al.45 displayed as a two-dimensional heatmap, superimposed with differentially methylated regions of cluster 10. The differentially methylated regions were analyzed with multiple window sizes as indicated (see Methods).
