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Table 5 DMPs with effect sizes ≥ 0.3 after stringent filtering

From: Epigenetic adaptations of the masticatory mucosa to periodontal inflammation

Probe ID Chr:Position (hg19) Distance to nearest significant DMP (bp) Sup-porting DMPs (n) Gene Symbol Median TPM* p (full analysis) q (full analysis) padj (paired analysis) ∆β (full analyis) Raw beta values (mean)
Uninflamed (n = 48) Inflamed (n = 48) pGECs (n = 5) Blood** (n = 69)
cg14991316 chr20:36,932,377 8 3 BPI 0 4.0 × 10–11 3.1 × 10–5 1.0 × 10–3 − 0.34 0.67 0.12 0.92 0.06
cg09514933 chr2:242,605,566 185 3 ATG4B 554 7.9 × 10–14 6.2 × 10–8 1.4 × 10–3 − 0.33 0.89 0.76 0.94 0.96
cg10539002 chr10:117,061,032 561 1 ATRNL1 22 9.5 × 10–11 7.4 × 10–5 1.3 × 10–3 − 0.31 0.53 0.28 0.42 0.67
cg11804639 chr8:97,056,896 523 1 GAPDHP30 NA 1.2 × 10–10 9.7 × 10–5 3.5 × 10–3 − 0.31 0.77 0.37 0.66 NA
cg15528852 chr7:41,137,006 40 1 LINC01449 NA 1.9 × 10–8 1.5 × 10–2 5.0 × 10–4 − 0.31 0.68 0.51 0.64 0.85
cg18450582 chr7:95,546,539 31 1 DYNC1I1 15 2.4 × 10–10 1.8 × 10–4 9.6 × 10–4 − 0.30 0.80 0.64 0.82 0.94
cg27130240 chr16:88,943,533 356 3 CBFA2T3 72 9.3 × 10–9 7.2 × 10–3 7.5 × 10–2 − 0.30 0.72 0.74 0.64 0.99
  1. DMPs meeting the following filter criteria: q < 0.05, distance to nearest significant (q < 0.05) DMPs \(\le\) 2 kb (= supporting DMPs), effect size ≥ 0.3, at least one DMP in cluster with padj paired < 0.05. 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
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Clinical Epigenetics

ISSN: 1868-7083

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