A finer analysis of the probe-level data focused on sequences with two consecutive probes defined as differentially methylated (±1.3-fold changed). These data were fit to a linear mixed model to account for sources of experimental variability as well as random error. As with the region-based analysis described above, similar patterns of promoter numbers were found to have increased or decreased methylation, with ~10% occurring in both NTC and NTO groups and ~45% occurring in only one of the groups. Upon splitting these into low or high CpG regions, there were greater effects in the NTO group than the NTC group. High CpG regions had more genes decreased and low CpG regions had more genes increased. Pathway analysis of these categorized gene sets identified affected functions including embryonic development, including genes specific for tissues such as heart, retina, sensory nervous system, and stem cell migration, all consistent with known phenotypes of FAS.
