Fig. 3

Network analysis of MT2 DNA methylation reveals importance of 3′ region. a Community structure network of CpG sites in MT2 containing three communities: community 1 (green) which contains 5′ CpGs, community 2 (orange) which contains mostly CpGs in the middle of MT2, and community 3 (blue) which contains mostly 3′ CpGs. The weight of edges indicates higher covariance between CpG sites. b Item stability scores for each CpG site. CpGs with scores greater than 0.8 are considered stable. c Animals raised by low care parents (MAN0) have higher standardized network community scores, which represent DNA methylation within the community (13 male–female sibling pairs; MAN0: n = 7 males, 7 females; MAN1: n = 6 males, 6 females; 2 way handling condition x community ANOVA, main effect of handling condition, F_{(1, 72)} = 22.41, p = 1.1e-5; no effect of community, F_{(2, 72)} = 0.001, p = .99. Follow-up t tests between handling conditions at each community were conducted with Bonferroni correction (*p < 0.05, **p < 0.01). Cohen’s d is provided to measure effect size.) The effect size of handling condition on standardized network community score is largest in community 3. d Standardized network community scores for each community are correlated with Oxtr gene expression using Spearman’s rank correlation; community 1: ρ = -0.29, p = 0.086; community 1: ρ = -0.37, p = 0.03; community 3: ρ = -0.47, p = 0.003