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 |