Extended Data Fig. 6: DNA methylation correlation functions in the mouse embryo.
From: Scaling and self-similarity in the formation of the embryonic epigenome
(a) Empirical and simulated correlation functions of DNA methylation for different stages of embryonic development. Error bars for the simulations indicate the standard deviation computed over 100 stochastic realizations of the master equation. Error bar for the experiments denotes average over all pairs of base pairs separated by the same genomic distance. The center of the dot is the average. Arrows indicate an enrichment of empirical correlations with respect to the model predictions. (b) Difference between simulated and empirical correlation function (residual) rescaled by the empirical standard error shown separately for each chromosome. Correlation functions were calculated for gene bodies corresponding to the bottom (left) and top (right) 2000 expressed genes. (c) Boxplots of average gene body methylation for both groups of genes (n = 2000 top and n = 2000 bottom expressed genes for each stage). The lower and upper hinges correspond to the first and third quartiles, respectively. The whiskers represent the range of the data up to 1.5 times the inter quartile range. The horizontal line indicates the median. Dots represent data points that deviate more than 1.5 times the inter quartile range from the median.
