Table 2.
Statistically Significant Differentially Methylated CpG Sites Between TP53 Mutation Carriers and Noncarriers
| Probe ID | Δβ* | P† | q‡ | CHR | MAPINFO | UCSC Gene Name |
|---|---|---|---|---|---|---|
| cg12385729 | −0.1045 | < .001 | 3.09E-15 | 1 | 9243679 | miR-34A (promoter) |
| cg06677321 | 0.1081 | < .001 | 1.33E-07 | 17 | 67603831 | |
| cg20116804 | −0.0649 | < .001 | 1.73E-06 | 6 | 48036212 | C6orf138 (PTCH53) |
| cg26371327 | −0.09 | < .001 | 5.17E-06 | 1 | 16473143 | EPHA2 |
| cg27582323 | −0.0576 | < .001 | 5.96E-05 | 1 | 16472728 | EPHA2 |
| cg26820168 | −0.0623 | < .001 | 1.59E-03 | 8 | 124217896 | FAM83A |
| cg19518666 | 0.095 | < .001 | 2.09E-03 | 4 | 157692845 | PDGFC |
| cg02242734 | −0.043 | < .001 | 3.44E-03 | 22 | 18064224 | SLC25A18 |
| cg00865857 | −0.0445 | < .001 | 4.13E-03 | 8 | 145926462 | |
| cg20048521 | −0.0503 | < .001 | 5.93E-03 | 6 | 74072242 | C6orf221 |
| cg27053337 | −0.0595 | < .001 | 6.95E-03 | 8 | 124217698 | FAM83A |
| cg21215576 | −0.0548 | < .001 | 6.95E-03 | 8 | 124217760 | FAM83A |
| cg04306069 | −0.048 | < .001 | 6.95E-03 | 5 | 98175255 | |
| cg25731261 | −0.0388 | < .001 | 9.25E-03 | 19 | 47736018 | BBC3 (PUMA) |
| cg06489965 | −0.0452 | < .001 | 1.08E-02 | 16 | 3062975 | CLDN9 |
| cg14395060 | 0.0628 | < .001 | 1.14E-02 | 22 | 32441170 | SLC5A1 |
| cg26140120 | −0.0639 | < .001 | 1.14E-02 | 8 | 124219575 | FAM83A |
| cg23467079 | −0.0692 | < .001 | 1.18E-02 | 8 | 124219425 | FAM83A |
| cg27612019 | −0.0434 | < .001 | 1.29E-02 | 22 | 18064052 | SLC25A18 |
| cg18165186 | −0.0369 | < .001 | 1.30E-02 | 3 | 50314180 | SEMA3B |
| cg00962755 | −0.0486 | < .001 | 1.33E-02 | 1 | 201439001 | PHLDA3 |
| cg07250758 | −0.0422 | < .001 | 1.55E-02 | 11 | 61049251 | VWCE |
| cg23252259 | −0.0764 | < .001 | 1.55E-02 | 6 | 31148612 | |
| cg07142285 | −0.0357 | < .001 | 1.55E-02 | 20 | 57042703 | APCDD1L |
| cg14731462 | 0.0664 | < .001 | 1.57E-02 | 10 | 129789429 | PTPRE |
| cg24869272 | −0.0632 | < .001 | 1.67E-02 | 11 | 850296 | TSPAN4 |
| cg22157494 | −0.0444 | < .001 | 1.88E-02 | 1 | 3774827 | KIAA0562 |
| cg17892917 | 0.0364 | < .001 | 1.88E-02 | 3 | 107823424 | |
| cg26550861 | −0.0505 | < .001 | 1.88E-02 | 6 | 74072376 | C6orf221 |
| cg18419358 | 0.0676 | < .001 | 2.32E-02 | 6 | 158384009 | |
| cg20296493 | −0.0476 | < .001 | 2.48E-02 | 8 | 124219725 | FAM83A |
| cg27500148 | −0.0228 | < .001 | 2.50E-02 | 17 | 37011491 | RPL23 |
| cg05192831 | −0.0338 | < .001 | 3.05E-02 | 16 | 29913007 | ASPHD1 |
| cg04284678 | −0.0451 | < .001 | 3.47E-02 | 14 | 105995251 | TMEM121 |
| cg06508738 | −0.0489 | < .001 | 3.47E-02 | 3 | 138763852 | PRR23C |
| cg04645534 | 0.0444 | < .001 | 3.49E-02 | 8 | 23712550 | STC1 |
| cg02625638 | −0.0338 | < .001 | 3.78E-02 | 8 | 124218648 | FAM83A |
| cg11498156 | −0.0403 | < .001 | 3.78E-02 | 10 | 102890145 | TLX1 |
| cg22989419 | 0.0482 | < .001 | 4.19E-02 | 20 | 9340396 | PLCB4 |
| cg21922810 | 0.0418 | < .001 | 4.30E-02 | 1 | 6669887 | |
| cg21385909 | −0.0555 | < .001 | 4.30E-02 | 15 | 31621843 | KLF13 |
| cg04715503 | −0.0873 | < .001 | 4.39E-02 | 16 | 3062795 | CLDN9 |
| cg22384356 | 0.0646 | < .001 | 4.63E-02 | 8 | 124195192 | FAM83A |
| cg00468228 | 0.0317 | < .001 | 4.79E-02 | 8 | 67092562 | |
| cg09658497 | 0.064 | < .001 | 4.80E-02 | 7 | 2847517 | GNA12 |
| cg13360823 | −0.0428 | < .001 | 4.82E-02 | 19 | 54496353 | CACNG6 |
| cg25962015 | 0.0314 | < .001 | 4.82E-02 | 7 | 26579291 | KIAA0087 |
| cg20401945 | −0.0409 | < .001 | 4.82E-02 | 16 | 29912460 | ASPHD1 |
| cg22291365 | −0.0446 | < .001 | 4.82E-02 | 15 | 74891439 |
Abbreviations: CHR, chromosome; MAPINFO, chromosomal coordinates on human genome assembly GRCh37/hg19; UCSC, University of California Santa Cruz.
*
Differential methylation level (Δβ) between TP53 mutation carriers relative to wild type.
†
P value determined by Mann-Whitney U test at each CpG site.
‡
Adjusted P value after Benjamini-Hochberg correction for false discovery rate.