Fig. 3

Oscillation profiles within epigenetically variable cytosines. a Heatmap of all FDR-significant EVCs with rows representing independent cytosines and columns representing samples ordered by CT. Missing CTs (CT31 and CT52) were replaced with the mean values of their two nearest neighbors. All cytosines were standardized using a z-score transformation. Hierarchical clustering with correlation distance grouped the cytosines into three clusters. Cosinor model fit on the averaged sample values is depicted below each cluster along with the cosinor p value. b Periodogram showing percentages of oscillating FDR EVCs using various oscillation periods. c Histogram of oscillation p values of nominally significant EVCs. d Percentage of oscillating nominally significant EVCs in 10,000 permutations of CT labels. The red line shows the observed percentage of oscillating cytosines in the unshuffled data. e Distribution of acrophases across significantly oscillating nominally significant EVCs. The gray shaded area indicates dark hours. f Average mesor values for osc-modCs peaking during light hours (red) and dark hours (blue). Shaded areas depict the 95% confidence interval for the mesor means. For illustration purposes, the mesor values were depicted using the average oscillation pattern within each group. CT, circadian time; modCs, modified cytosines; EVCs, epigenetically variable cytosines