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Table 3. 20 DMPs with highest effect sizes

From: Epigenetic adaptations of the masticatory mucosa to periodontal inflammation

Probe ID Chr:Position (hg19) Distance to nearest significant DMP (bp) Gene Symbol Median TPM* p (full analysis) q (full analysis) padj (paired analysis) β (full analysis) Raw beta values (mean)
Uninflamed (n = 48) Inflamed (n = 48) pGECs (n = 5) Blood (n = 69)**
cg11303839 chr7:75,405,967 84,519 CCL26 10 5.1 × 10–12 4.0 × 10–6 4.0 × 10–4 − 0.43 0.64 0.18 0.61 0.31
cg16307144 chr19:38,704,933 14,590 DPF1 6 4.7 × 10–11 3.6 × 10–5 0.012 − 0.40 0.68 0.31 0.57 0.66
cg08670006 chr14:56,738,739 154,092 PELI2 66 3.6 × 10–11 2.8 × 10–5 1.5 × 10–3 − 0.37 0.52 0.27 0.30 0.86
cg26189827 chr7:40,338,925 11,044 SUGCT 45 2.3 × 10–12 1.8 × 10–6 2.1 × 10–3 − 0.37 0.57 0.18 0.08 0.38
cg03606473 chr3:102,846,710 1,035,074 gene desert NA 1.1 × 10–10 8.2 × 10–5 7.4 × 10–5 − 0.37 0.57 0.27 0.35 0.76
cg04025284 chr14:60,636,610 336,907 DHRS7 460 2.2 × 10–10 1.7 × 10–4 3.8 × 10–3 − 0.37 0.79 0.68 0.80 0.90
cg25249713 chr4:177,045,356 28,224 WDR17 9 2.2 × 10–10 1.7 × 10–4 0.016 − 0.37 0.78 0.35 0.88 0.83
cg10659908 chr12:109,796,147 66,574 LINC01486 NA 3.3 × 10–13 2.6 × 10–7 6.9 × 10–4 − 0.36 0.70 0.30 0.85 0.54
cg07804660 chr11:266,869 22,085 gene desert NA 3.3 × 10–11 2.6 × 10–5 1.8 × 10–4 − 0.36 0.72 0.40 0.80 0.79
cg24852319 chr6:113,278,378 266,486 gene desert NA 2.1 × 10–11 1.7 × 10–5 1.2 × 10–4 − 0.36 0.71 0.36 0.55 0.83
cg27171156 chr2:71,698,651 4367 DYSF 92 5.6 × 10–9 4.4 × 10–3 1.8 × 10–3 − 0.36 0.61 0.31 0.11 0.79
cg27531927 chr13:98,598,462 29,598 gene desert NA 2.5 × 10–8 0.020 3.0 × 10–3 − 0.36 0.61 0.27 0.23 0.74
cg09168806 chr8:97,056,373 523 gene desert NA 2.8 × 10–9 2.2 × 10–3 2.7 × 10–3 − 0.35 0.61 0.30 0.24 0.75
cg01306824 chr17:77,834,118 18,952 gene desert NA 2.5 × 10–15 2.0 × 10–9 0.010 − 0.35 0.63 0.50 0.67 0.94
cg01658895 chr5:74,621,313 11,545 gene desert NA 1.4 × 10–9 1.1 × 10–3 1.2 × 10–5 − 0.35 0.63 0.42 0.76 0.84
cg02061660 chr5:110,088,130 12,074 SLC25A46 747 5.1 × 10–8 0.039 5.8 × 10–4 − 0.35 0.68 0.40 0.70 0.84
cg09605880 chr1:32,397,195 7131 PTP4A2 1034 1.1 × 10–10 8.5 × 10–5 2.8 × 10–3 − 0.34 0.51 0.21 0.47 0.52
cg12859373 chr6:90,993,998 203,279 BACH2 135 2.3 × 10–8 0.017 7.0 × 10–3 − 0.34 0.54 0.10 0.24 0.14
cg14991316 chr20:36,932,377 8 BPI 0 4.0 × 10–11 3.1 × 10–5 1.0 × 10–3 − 0.34 0.67 0.12 0.92 0.06
cg19996026 chr10:69,455,804 262,127 CTNNA3 2 5.2 × 10–10 4.1 × 10–4 1.7 × 10–3 − 0.34 0.67 0.35 0.66 NA
  1. DMPs with the highest effect sizes from the full analysis that also showed a significant association in the paired sub-analysis. p Values from paired analysis are Bonferroni-corrected for 15,507 tests. ∆β-values are adjusted according to our intercept method [16]. *mRNA-sequencing in healthy keratinized oral mucosa with 16mio reads/sample [12]. **downloaded from GSE123914 [54]. DMP = differentially methylated position, bp = basepairs, TPM = transcripts per million, pGECs = primary gingival epithelial cells