Among the top 20 genes exhibiting β-threshold-based directionality changes, 13 were significantly enriched in GO terms: 8 in the Control low → Periodontitis high group (DGKA, CHMP6, RUNX2, CDKL1, SLC6A3, CFTR, HLA-C, LRIG1), 5 in the Control high → Periodontitis low group (AP2A2, PARD3, PADI2, FOXK1, RGS1).<h4>Conclusions</h4>This study provides an exploratory, direction-aware summary framework of DNA methylation in periodontitis, highlighting functional changes beyond CpG islands and identifying candidate genes for further functional validation. Here, PADI2 is linked to periodontitis.