In many case, “functional” changes in DNA methylation may occur in a short stretch of a promoter CpG island. Thus, instead of analyzing an average methylation change for an entire promoter, we discerned the DNA methylation level changes at a two-consecutive probe-level (same direction change of two probes stretched over 150 nucleotides) (see Methods). A linear mixed-effect model was used to analyze the alcohol-induced methylation changes along the promoter region (see Methods) by comparing control vs. ALC-NTO (neural tube open), and control vs. ALC-NTC (neural tube closed).
