Table 3.

Cancer-associated CpGs in TRGs by pathway at FDR < 0.05

PathwayGeneCpGRegionIslandβa95% CIFDR
HelicasePIF1cg110137265′UTRIsland1.000.57–1.430.02
RECQL4cg17368874TSS200Island6.673.13–10.200.04
ShelterinACDcg04265926TSS1500Island6.673.09–10.250.04
TINF2cg022711801stExonIsland1.990.88–3.100.05
TelomeraseDKC1cg19944582TSS200Island5.802.74–8.850.04
WRAP53cg25053252TSS1500Island5.472.82–8.120.03
RepairBTBD12cg04157159TSS200Island4.251.92–6.580.04
DCLRE1Ccg14369264TSS1500Island1.110.53–1.690.04
DCLRE1Ccg24866702TSS200Island6.533.12–9.950.04
DCLRE1Ccg04785461TSS200Island5.382.37–8.400.05
DDB1cg230539181stExonIsland5.452.75–8.150.03
DDB1cg20772347TSS200Island5.682.65–8.720.04
DDB1cg24840365TSS200Island5.492.55–8.430.04
DDB1cg255306311stExonIsland6.633.04–10.220.04
DDB1cg087249191stExonIsland1.450.64–2.260.05
FEN1cg25628257TSS200Island3.952.03–5.870.03
HMBOX1cg14143435TSS200N_Shore1.410.73–2.100.03
MSH2cg005477585′UTRIsland6.232.97–9.480.04
PARP3cg14974841TSS1500Island5.222.49–7.950.04
PARP3cg14262432TSS200Island6.933.00–10.860.05
RAD51L3cg19223675TSS200S_Shore5.162.27–8.050.05
RAD54Lcg24955114TSS1500OpenSea6.162.67–9.660.05
SIRT6cg150344645′UTRIsland5.112.78–7.440.03
OtherBICD1cg21587861TSS200Island6.933.12–10.750.04
CLPTM1Lcg197392641stExonIsland4.892.37–7.410.04
MAD1L1cg09776772BodyOpenSea-0.65−0.97 to −0.330.03
MAD1L1cg13247668TSS200Island5.002.30–7.710.04
MTRRcg266279331stExonIsland5.452.73–8.160.03
MYCcg07871324TSS1500Island5.812.91–8.710.03
RTEL1cg27236539TSS200Island1.250.56–1.940.04
SIP1cg15533434TSS200Island5.282.48–8.090.04
  • aBeta coefficients represent the average difference in methylation (M-value) between cases and controls.