SMN2 CGI 3 was hypomethylated (mean methylation levels <10%) with a single outlier at nt position +89, while SMN2 CGI 2 displayed intermediate mean methylation levels.
However, mean methylation levels were largely comparable between recipients and donors.
Only mean methylation levels, and not individual methylation data, can be obtained from pooled samples.
Table 3 displays mean methylation levels for each gene and the correlation between the two sites.
Additional analyses examined potential confounders of gender and mean methylation levels.
Usually, after quality control step and normalisation of the dataset, mean methylation levels are calculated for each CpG site and are compared between groups of subjects in order to identify significant differences or correlations.
Girl and boy mean methylation levels are shown on the β value or % methylation aPositions shown for hg19 (Genome Reference Consortium GRCh37) genome assembly Counts of all, hypermethylated, and hypomethylated autosomal CpGs associated with sex in newborns by proximity to CpG island and gene features.
Of the samples that showed more than 1 % methylation in the UNC5C promoter, mean methylation levels of UNC5C were significantly higher in gastric cancers compared with their corresponding normal gastric mucosa specimens (17.4 % (95 % CI, 12.4 22.4 %] in gastric cancers; 6.3 % (95 % CI, 3.1 9.5 %] in normal gastric mucosa specimens; P < 0.0001, Wilcoxon/Kruskal Wallis test; Fig. 3c d).
Given the low numbers of participants in some of these strata, we used Fisher's exact tests to determine if methylation status (above vs. below median) differed between the three groups for each of the 6 loci (Table 6; mean methylation levels are presented in Supplemental Table 6 in Additional file 1).
Furthermore, among those not on antidepressants, placental methylation at this locus differed between the following 3 groups: 1) those with no history of psychiatric disease, 2) those with a history but no active disease, and 3) those with a history and active disease (Table 7, Fisher's exact test p = 4.8 × 10−4, mean methylation levels are presented in Supplemental Table 7 in Additional file 1).
The remaining tissues demonstrated partial mean methylation levels; more specifically, saliva − 0.43, vaginal fluid − 0.22 and menstrual blood − 0.22.
