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. 2016 May 12;8:54. doi: 10.1186/s13148-016-0219-0

Table 2.

Significant mediating effects of gene methylation on IFN-γ outcome

Gene CpG site DNA methylation IFN-γ outcome Mediation effect
R 2 Storm32 R 2 DNA methylation Storm32
Effect (a) SE p val. Effect (b) SE p val. Effect (c') SE p val. Effect (a*b) Boot SE Boot LLCI Boot ULCI Standardized effect
DDR1 cg11975790 0.1813 0.0527 0.0201 0.0135 0.1749 −0.4065 0.1856 0.0364 0.0474 0.0230 0.0478 −0.0214 0.0116 −0.0537 −0.0045 −0.170991
FLT1 cg24850711 0.2527 0.0606 0.0187 0.0029 0.1142 −0.3210 0.2065 0.1306 0.0454 0.0249 0.0782 −0.0195 0.0129 −0.0540 −0.0010 −0.155283
IGF1R cg13297560 0.1322 0.0388 0.0178 0.0375 0.1376 −0.3883 0.2139 0.0795 0.0410 0.0228 0.0822 −0.0151 0.0113 −0.0475 −0.0007 −0.120139
IL1R2 cg12910851 0.1628 0.0353 0.0144 0.0199 0.2001 −0.6216 0.2560 0.0214 0.0479 0.0224 0.0406 −0.0219 0.0151 −0.0659 −0.0031 −0.174821
LCK cg17078393 0.2561 0.0659 0.0202 0.0027 0.1783 −0.4104 0.1846 0.0339 0.0530 0.0241 0.0353 −0.0271 0.0139 −0.0640 −0.0055 −0.21591
cg05350315 0.1949 0.0711 0.0260 0.0101 0.1651 −0.3033 0.1447 0.0447 0.0475 0.0233 0.0503 −0.0216 0.0145 −0.0629 −0.0019 −0.172012
cg11683242 0.1681 0.0443 0.0177 0.0178 0.2545 −0.5858 0.2007 0.0066 0.0519 0.0217 0.0231 −0.0259 0.0126 −0.0599 −0.0073 −0.206796
cg14781242 0.2081 0.0505 0.0177 0.0076 0.1625 −0.4395 0.2124 0.0472 0.0482 0.0235 0.0495 −0.0222 0.0109 −0.0519 −0.0063 −0.177247
LTA cg16280132 0.3331 0.0652 0.0166 0.0004 0.1463 −0.4366 0.2291 0.0663 0.0544 0.0259 0.0440 −0.0285 0.0152 −0.0654 −0.0047 −0.227195
cg09736959 0.2952 0.0758 0.0210 0.0011 0.1433 −0.3391 0.1809 0.0706 0.0517 0.0252 0.0494 −0.0257 0.0150 −0.0628 −0.0014 −0.20498
cg24216966 0.2611 0.0886 0.0268 0.0024 0.1401 −0.2620 0.1423 0.0755 0.0492 0.0247 0.0555 −0.0232 0.0144 −0.0628 −0.0022 −0.185282
cg01157951 0.2634 0.0663 0.0199 0.0023 0.1334 −0.3402 0.1922 0.0869 0.0485 0.0248 0.0600 −0.0225 0.0140 −0.0592 −0.0010 −0.179876
cg21999229 0.2593 0.1120 0.0340 0.0025 0.1287 −0.1940 0.1129 0.0961 0.0477 0.0248 0.0643 −0.0217 0.0142 −0.0592 −0.0002 −0.17327
cg14597739 0.2618 0.1198 0.0361 0.0023 0.1504 −0.2043 0.1049 0.0608 0.0504 0.0246 0.0487 −0.0245 0.0156 −0.0674 −0.0021 −0.195257
cg16219283 0.2575 0.1038 0.0316 0.0026 0.1430 −0.2250 0.1202 0.0710 0.0493 0.0246 0.0540 −0.0234 0.0151 −0.0641 −0.0010 −0.186303
cg13815684 0.2571 0.0877 0.0268 0.0026 0.1569 −0.2838 0.1410 0.0531 0.0509 0.0244 0.0456 −0.0249 0.0141 −0.0635 −0.0038 −0.198557
cg10476003 0.2229 0.0794 0.0266 0.0055 0.1749 −0.3071 0.1402 0.0364 0.0504 0.0236 0.0410 −0.0244 0.0138 −0.0656 −0.0048 −0.194562
cg09621572 0.2220 0.1022 0.0343 0.0056 0.1447 −0.2091 0.1107 0.0686 0.0473 0.0240 0.0578 −0.0214 0.0141 −0.0609 −0.0024 −0.170417
cg17169196 0.2233 0.0894 0.0299 0.0055 0.1638 −0.2615 0.1255 0.0459 0.0493 0.0237 0.0464 −0.0234 0.0138 −0.0624 −0.0042 −0.186458
cg02402436 0.2261 0.0932 0.0310 0.0052 0.1323 −0.2173 0.1236 0.0890 0.0462 0.0242 0.0661 −0.0203 0.0129 −0.0574 −0.0018 −0.161559
cg14441276 0.2038 0.0741 0.0263 0.0084 0.1409 −0.2678 0.1448 0.0742 0.0458 0.0238 0.0634 −0.0199 0.0136 −0.0591 −0.0010 −0.158425
cg11586857 0.1575 0.0561 0.0233 0.0222 0.1857 −0.3647 0.1590 0.0290 0.0464 0.0225 0.0477 −0.0205 0.0123 −0.0566 −0.0033 −0.163339
cg14437551 0.1758 0.0986 0.0383 0.0151 0.1758 −0.2304 0.0961 0.0230 0.0487 0.0226 0.0393 −0.0227 0.0140 −0.0635 −0.0035 −0.181167
LTBR cg23079808 0.1487 −0.0474 0.0204 0.0267 0.2281 0.4754 0.1772 0.0118 0.0485 0.0218 0.0337 −0.0225 0.0123 −0.0521 −0.0046 −0.179865
MAP3K14 cg16826777 0.1665 −0.0516 0.0207 0.0184 0.2136 0.4488 0.1759 0.0161 0.0491 0.0222 0.0349 −0.0231 0.0123 −0.0568 −0.0055 −0.184658
NFKBIA cg00689225 0.2086 0.0668 0.0234 0.0075 0.2304 −0.4173 0.1544 0.0112 0.0538 0.0226 0.0236 −0.0279 0.0127 −0.0630 −0.0095 −0.222303
cg16518861 0.1288 0.0439 0.0205 0.0403 0.2475 −0.4968 0.1740 0.0077 0.0478 0.0213 0.0322 −0.0218 0.0127 −0.0579 −0.0046 −0.173912
PIK3CD cg01320698 0.3012 0.0487 0.0133 0.0009 0.2948 −0.8481 0.2591 0.0027 0.0673 0.0230 0.0065 −0.0413 0.0172 −0.0857 −0.0155 −0.329546
cg07499142 0.1747 0.0599 0.0234 0.0155 0.1688 −0.3416 0.1603 0.0413 0.0464 0.0230 0.0522 −0.0205 0.0109 −0.0480 −0.0034 −0.163265
PIK3R2 cg11953794 0.2101 −0.0753 0.0262 0.0073 0.2804 0.4185 0.1330 0.0037 0.0575 0.0218 0.0133 −0.0315 0.0134 −0.0659 −0.0109 −0.251347
cg04610450 0.1700 −0.0442 0.0176 0.0171 0.2369 0.5647 0.2045 0.0097 0.0510 0.0219 0.0272 −0.0250 0.0127 −0.0600 −0.0068 −0.199292
PRKCZ cg02481000 0.1183 −0.0434 0.0213 0.0501 0.1988 0.4175 0.1728 0.0220 0.0441 0.0218 0.0523 −0.0181 0.0120 −0.0530 −0.0024 −0.14457
TGFBR2 cg04916416 0.1641 0.0412 0.0167 0.0193 0.1691 −0.4793 0.2246 0.0411 0.0457 0.0228 0.0543 −0.0197 0.0114 −0.0514 −0.0032 −0.157375
TLR6 cg14578677 0.1978 −0.0707 0.0256 0.0095 0.1637 0.3060 0.1470 0.0460 0.0476 0.0234 0.0506 −0.0216 0.0130 −0.0563 −0.0029 −0.172535
TNFAIP3 cg22014112 0.1467 0.0563 0.0244 0.0278 0.1868 −0.3499 0.1519 0.0284 0.0457 0.0223 0.0497 −0.0197 0.0131 −0.0576 −0.0024 −0.157265
TNFRSF1B cg05599723 0.1221 −0.0465 0.0224 0.0462 0.1850 0.3790 0.1657 0.0294 0.0436 0.0221 0.0573 −0.0176 0.0111 −0.0496 −0.0024 −0.140605
cg15526535 0.1349 0.0389 0.0177 0.0355 0.1947 −0.4959 0.2086 0.0240 0.0453 0.0221 0.0493 −0.0193 0.0113 −0.0496 −0.0038 −0.153835
cg22677556 0.2258 0.0679 0.0226 0.0052 0.1711 −0.3567 0.1656 0.0394 0.0502 0.0237 0.0424 −0.0242 0.0107 −0.0539 −0.0084 −0.193363
TRAF5 cg10721755 0.1654 −0.0516 0.0208 0.0188 0.2716 0.5175 0.1686 0.0045 0.0527 0.0214 0.0198 −0.0267 0.0140 −0.0644 −0.0070 −0.212858
ZAP70 cg08859278 0.1844 0.0475 0.0179 0.0126 0.2533 −0.5756 0.1979 0.0068 0.0533 0.0219 0.0211 −0.0273 0.0135 −0.0627 −0.0073 −0.2181

Mediation effects that survived Bonferroni correction are presented in italics

BCL10 B cell CLL/lymphoma 10, DDR1 discoidin domain receptor tyrosine kinase 1, FLT1 Fms-related tyrosine kinase 1, IGF1R insulin-like growth factor 1 receptor, IL1R2 interleukin 1 receptor, type II, LCK lymphocyte-specific protein tyrosine kinase, LTA lymphotoxin alpha, LTBR lymphotoxin beta receptor (TNFR superfamily, member 3), MAP3K14 mitogen-activated protein kinase kinase kinase 14, MAP4K4 mitogen-activated protein kinase kinase kinase kinase 4, NFKBIA nuclear factor of kappa light polypeptide gene enhancer in B cell inhibitor, alpha, PIK3CD phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta, PIK3R2 phosphoinositide-3-kinase, regulatory subunit 2 (beta), PRKCZ protein kinase C, zeta, TGFBR2 transforming growth factor, beta receptor II, TLR6 Toll-like receptor 6, TNFAIP3 tumor necrosis factor, alpha-induced protein 3, TNFRSF1B tumor necrosis factor receptor superfamily, member 1B, TRAF5 TNF receptor-associated factor 5, ZAP70 zeta-chain (TCR)-associated protein kinase 70 kDa, SE standard error, LLCI lower limit confidence interval, ULCI upper limit confidence interval