Despite the high heterogeneity, application of a random effects model suggested that global autosomal methylation was nominally higher in males than in females (mean beta difference = 48.9, P = 0.049).
The mean beta difference between sexes for the 184 statistically significant probes was 0.037 (3.7%, Additional file 2: Table S4), with the vast majority of associated CpG sites (n = 178, 97%) more methylated in females than in males.
The performance of individual statistical models was gauged by their overall R values (corresponding to variance explained by factors in the model), while the impact of individual factors was measured by the regression beta (adjusted mean beta difference, Δ β, and standard error, SE).
In line with previous studies, average beta differences were small.
We assessed the methylation levels of 366,074 variable CpG sites and found 28,917 CpG sites (annotated to 12,619 unique genes) that showed a significant difference (absolute mean beta value difference > 0.2, FDR < 0.05) between fetal and adult liver tissue (see Supplementary Online Methods in the Additional files 1 and 2).
We identified a total of 11 CpGs differentially methylated between the laboratories/platforms (p-value <0.01 and difference between mean beta values >0.2).
We then compared the mean per CpG in each group with the mean per CpG in each of the other groups and identified genes showing differential methylation (defined as a difference of mean Beta values above 0.5) (Figure 1).
While we did not observe any difference in mean beta cell size in human pregnancy, beta cells, interestingly, were on average larger in the post-partum period, perhaps reflecting the accumulation of granules with a decreased secretory burden per beta cell, since beta cell numbers did not undergo as rapid a decrease in humans as previously reported in rodents after pregnancy [ 4].
There was no significant difference in the mean beta values at SREBF2.
The Beta differences between the estimated means, adjusted for age, ICV and gender, for the two groups were calculated, as their corresponding P-values.
