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Table 8 Differentially methylated genes within the gene ontology term “synaptic vesicle cycle” (biological process)

From: Epigenetic adaptations of the masticatory mucosa to periodontal inflammation

Gene Full name TPM* Probe ID Chr:Pos (hg19) Regulatory features** β (full analysis) p (full analysis) q (full analysis) padj paired **
CLCN3 Chloride Voltage-Gated Channel 3 2771 cg11022756 chr4:170,540,250 PF − 0.14 6.0 × 10–16 4.8 × 10–10 6.9 × 10–3
RIMS1 Regulating Synaptic Membrane Exocytosis 1 0 cg21984541 chr6:72,795,650 R − 0.27 1.0 × 10–13 7.9 × 10–8 3.1 × 10–4
SNAP23 Synaptosome Associated Protein 23 615 cg13922935 chr15:42,804,870 T, R*** − 0.20 1.7 × 10–12 1.3 × 10–6 1.0 × 10–5
SYT9 Synaptotagmin 9 78 cg21672572 chr11:7,369,177 R − 0.33 4.2 × 10–12 3.3 × 10–6 4.7 × 10–5
STX1B Syntaxin 1B 21 cg05787209 chr16:31,022,521 R, E − 0.19 6.9 × 10–12 5.4 × 10–6 0.03
SYN3 Synapsin III 1 cg16894211 chr22:33,403,542 R − 0.24 1.6 × 10–11 1.3 × 10–5 1.6 × 10–3
SYT2 Synaptotagmin 2 1 cg03532262 chr1:202,587,916 R, WE − 0.17 2.7 × 10–11 2.1 × 10–5 4.5 × 10–4
SLC17A8 Solute Carrier Family 17 Member 8 0 cg03817774 chr12:100,772,630 R − 0.28 3.4 × 10–11 2.7 × 10–5 2.7 × 10–3
SYNDIG1 Synapse Differentiation Inducing 1 5 cg04332507 chr20:24,475,147 R, T − 0.15 5.8 × 10–11 4.6 × 10–5 0.05
RIMS2 Regulating Synaptic Membrane Exocytosis 2 4 cg23568361 chr8:104,862,936 R − 0.20 8.7 × 10–11 6.8 × 10–5 2.2 × 10–3
CADPS Calcium Dependent Secretion Activator 12 cg17149019 chr3:62,432,102 R − 0.14 2.7 × 10–10 2.1 × 10–4 3.4 × 10–3
UNC13C Unc-13 Homolog C 6 cg15450958 chr15:54,812,261 R, T, E − 0.22 1.2 × 10–9 9.7 × 10–4 0.04
CPLX1 Complexin 1 6 cg16649791 chr4:816,968 R − 0.25 1.5 × 10–9 1.2 × 10–3 4.5 × 10–3
SYT9 Synaptotagmin 9 78 cg07649045 chr11:7,260,764 R − 0.13 1.6 × 10–9 1.3 × 10–3 1.3 × 10–4
ERC2 ELKS/RAB6-Interacting/CAST Family Member 2 62 cg24265969 chr3:55,654,481 E, R − 0.32 2.1 × 10–9 1.6 × 10–3 0.05
PLD1 Phospholipase D1 1469 cg06085579 chr3:171,509,822 TSS, E, T, WE − 0.17 3.1 × 10–9 2.4 × 10–3 1.3 × 10–3
SYT7 Synaptotagmin 7 103 cg05131646 chr11:61,324,780 R, WE − 0.12 3.4 × 10–9 2.7 × 10–3 8.7 × 10–3
SYT12 Synaptotagmin 12 6 cg13851621 chr11:66,812,262 R, CTCF − 0.19 3.6 × 10–9 2.8 × 10–3 7.7 × 10–3
RAB3B RAB3B, Member RAS Oncogene Family 14 cg01223789 chr1:52,392,189 CTCF − 0.23 3.8 × 10–9 3.0 × 10–3 4.5 × 10–3
SLC17A8 Solute Carrier Family 17 Member 8 0 cg17713193 chr12:100,803,749 R − 0.22 4.6 × 10–9 3.6 × 10–3 0.05
SYT1 Synaptotagmin 12 12 cg16495154 chr12:79,802,105 CTCF, E − 0.18 5.9 × 10–9 4.6 × 10–3 4.4 × 10–3
SYNJ2 Synaptojanin 2 251 cg19920417 chr6:158,468,344 R, T, WE − 0.21 7.4 × 10–9 5.8 × 10–3 9.2 × 10–3
BSN Bassoon Presynaptic Cytomatrix Protein 7 cg20796968 chr3:49,700,419 R − 0.09 1.3 × 10–8 0.01 0.01
CPLX2 Complexin 2 5 cg14416206 chr5:175,247,405 R − 0.18 1.3 × 10–8 0.01 2.9 × 10–3
DDC Dopa Decarboxylase 0 cg08241694 chr7:50,633,896 R, PF − 0.14 1.5 × 10–8 0.01 0.03
RIMS1 Regulating Synaptic Membrane Exocytosis 1 0 cg26298612 chr6:73,074,746 R − 0.11 2.1 × 10–8 0.02 2.9 × 10–3
DNM1L Dynamin 1 Like 867 cg08823831 chr12:32,871,622 T − 0.16 2.1 × 10–8 0.02 7.8 × 10–3
SYT7 Synaptotagmin 7 103 cg02284433 chr11:61,280,813 R, WE − 0.13 5.3 × 10–8 0.04 0.04
PRKAR1B Protein Kinase CAMP-Dependent Type I Regulatory Subunit β 176 cg26669717 chr7:641,028 R, T, TSS − 0.11 5.7 × 10–8 0.04 0.04
CADPS Calcium Dependent Secretion Activator 12 cg03546671 chr3:62,789,196 R − 0.15 5.8 × 10–8 0.04 6.3 × 10–3
  1. Genes from the gene ontology term “synaptic vesicle cycle” with significant DMPs [q (full analysis) ≤ 0.05 and padj (paired) ≤ 0.05], sorted by p values (full analysis). ∆β-values are adjusted according to our intercept method [16]. *mRNA-sequencing in healthy keratinized oral mucosa with 16mio reads/sample [12]. **Based on Chip-Seq Data from the ENCODE project. ***in H1-hESC (H1 human embryonic stem cell line) only. TSS = Predicted promoter region including transcription start site, PF = Predicted promoter flanking region, E = Predicted enhancer, WE = Predicted weak enhancer or open chromatin cis regulatory element, CTCF = CTCF enriched element, T = Predicted transcribed region, R = Predicted repressed or low activity region