Table 3. Top 20 differentially methylated CpGs in iMT/iLT subchondral bone.
| Illumina ID | Associated Gene | iLT mean β (SD) | iMT mean β (SD) | Mean △β | FDR-p value |
|---|---|---|---|---|---|
| Hypermethylated | |||||
| cg19346371 | TBX3 | 0.5020 (0.1141) | 0.2397 (0.0754) | −0.2622 | 4.91E-03 |
| cg23229261 | OTX1 | 0.7226 (0.0638) | 0.4860 (0.1139) | −0.2367 | 5.50E-03 |
| cg24039697 | FLJ45983 | 0.5550 (0.0895) | 0.3294 (0.0989) | −0.2256 | 1.14E-02 |
| cg21472506 | OTX1 | 0.7586 0.0516) | 0.5504 (0.1136) | −0.2082 | 8.00E-03 |
| cg15526081 | 0.6311 0.0721) | 0.4256 (0.1062) | −0.2056 | 1.65E-02 | |
| cg04937416 | PTPRN2 | 0.5263 0.0710) | 0.3456 (0.0707) | −0.1807 | 8.74E-03 |
| cg13630043 | EMX2 | 0.6428 0.0582) | 0.4670 (0.0842) | −0.1758 | 9.97E-03 |
| cg09334277 | 0.6822 (0.0668) | 0.5078 (0.0574) | −0.1744 | 4.18E-03 | |
| cg03301200 | 0.5306 (0.0367) | 0.3564 (0.0852) | −0.1742 | 5.92E-03 | |
| cg02019574 | 0.5718 (0.0443) | 0.3992 (0.1109) | −0.1726 | 3.96E-02 | |
| cg08451832 | 0.4794 (0.0875) | 0.3068 (0.0737) | −0.1726 | 3.34E-02 | |
| cg03993743 | SIM2 | 0.6249 (0.0610) | 0.4567 (0.0983) | −0.1681 | 3.35E-02 |
| cg18561589 | EMX2OS | 0.6227 (0.0584) | 0.4553 (0.0843) | −0.1675 | 1.44E-02 |
| cg06141846 | EMX2OS | 0.5493 (0.0725) | 0.3833 (0.0725) | −0.1660 | 1.72E-02 |
| cg03311684 | EMX2OS | 0.6492 (0.0639) | 0.4878 (0.0648) | −0.1615 | 8.61E-03 |
| cg27630311 | TBX3 | 0.4143 (0.0827) | 0.2532 (0.0717) | −0.1611 | 3.08E-02 |
| cg21608600 | 0.5253 (0.0326) | 0.3644 (0.0968) | −0.1610 | 1.81E-02 | |
| cg00756451 | TBX5 | 0.4787 (0.0481) | 0.3177 (0.0521) | −0.1609 | 1.60E-03 |
| cg12121660 | HOXB2 | 0.6276 (0.0443) | 0.4698 (0.0799) | −0.1579 | 9.97E-03 |
| cg15572489 | PTPRN2 | 0.5116 (0.0619) | 0.3555 (0.0719) | −0.1562 | 1.55E-02 |
| Hypermethylated | |||||
| cg20307896 | 0.4289 (0.0567) | 0.6071 (0.0588) | 0.1781 | 1.97E-03 | |
| cg16856049 | 0.4274 (0.0643) | 0.6078 (0.0777) | 0.1804 | 9.49E-03 | |
| cg05259508 | 0.4211 (0.0779) | 0.6021 (0.0442) | 0.1810 | 3.99E-03 | |
| cg17616537 | HOXB3 | 0.5390 (0.0562) | 0.7214 (0.0748) | 0.1825 | 3.66E-03 |
| cg07080050 | HOXC4 | 0.3924 (0.0555) | 0.5762 (0.0369) | 0.1838 | 3.96E-04 |
| cg02458062 | HOXB3 | 0.6429 (0.0534) | 0.8307 (0.0855) | 0.1878 | 4.02E-03 |
| cg21229570 | 0.5882 (0.1032) | 0.7760 (0.0359) | 0.1878 | 9.06E-03 | |
| cg15772924 | HOXC4; HOXC5; HOXC6 | 0.4023 (0.0505) | 0.5923 (0.0373) | 0.1900 | 1.95E-04 |
| cg18470839 | 0.5661 (0.0661) | 0.7574 (0.0383) | 0.1913 | 5.75E-04 | |
| cg18220920 | 0.4180 (0.0794) | 0.6126 (0.0520) | 0.1945 | 3.60E-03 | |
| cg01529365 | 0.2868 (0.0619) | 0.4882 (0.0684) | 0.2014 | 2.11E-03 | |
| cg18197377 | 0.4571 (0.0871) | 0.6607 (0.0588) | 0.2036 | 5.66E-03 | |
| cg14283944 | 0.2543 (0.0540) | 0.4588 (0.0848) | 0.2045 | 2.52E-03 | |
| cg19175386 | 0.4625 (0.0830) | 0.6733 (0.0670) | 0.2107 | 4.38E-03 | |
| cg24208826 | 0.2459 (0.0884) | 0.4590 (0.0846) | 0.2131 | 1.16E-02 | |
| cg25340966 | TBX15 | 0.3968 (0.0680) | 0.6143 (0.0865) | 0.2174 | 3.92E-03 |
| cg10308785 | HOXB6; LOC404266 | 0.3427 (0.1107) | 0.5691 (0.0891) | 0.2264 | 1.89E-02 |
| cg26127662 | HOXA3 | 0.4790 (0.0898) | 0.7057 (0.0621) | 0.2267 | 2.79E-03 |
| cg24672833 | 0.2681 (0.0923) | 0.5132 (0.1168) | 0.2452 | 1.92E-02 | |
| cg10703826 | TBX15 | 0.3675 (0.0649) | 0.6268 (0.1081) | 0.2593 | 2.98E-03 |