Table 2.
Top-ranked differentially methylated CpGs in prostate cancer versus adjacent benign tissuea
| CpG ID | Chromosome | Gene | Location | CpG island | Mean β cancer |
Mean β benign |
Mean β difference |
Q-value |
|---|---|---|---|---|---|---|---|---|
| cg26027669 | 1 | GFI1 | TSS1500 | Yes | 0.61 | 0.16 | 0.45 | 6.84E-06 |
| cg18755783 | 13 | SPG20 | 5'UTR | Yes | 0.64 | 0.20 | 0.43 | 1.97E-04 |
| cg07016276 | 6 | HLA-F | Body | Yes | 0.62 | 0.19 | 0.43 | 2.35E-04 |
| cg01404317 | 13 | SPG20 | 5'UTR | Yes | 0.69 | 0.28 | 0.42 | 2.35E-04 |
| cg19548479 | 17 | TMEM106A | TSS200 | Yes | 0.67 | 0.22 | 0.44 | 2.47E-04 |
| cg15472092 | 7 | KCNH2 | TSS200 | Yes | 0.66 | 0.25 | 0.41 | 2.47E-04 |
| cg03049782 | 17 | TMEM106A | TSS200 | Yes | 0.64 | 0.21 | 0.43 | 2.47E-04 |
| cg24940138 | 17 | TMEM106A | TSS200 | Yes | 0.63 | 0.22 | 0.41 | 3.28E-04 |
| cg08193650 | 2 | ZFP36L2 | Body | Yes | 0.57 | 0.16 | 0.41 | 3.31E-04 |
| cg08952506 | 2 | AOX1 | TSS200 | Yes | 0.62 | 0.21 | 0.41 | 3.31E-04 |
| cg07564962 | 5 | – | – | Yes | 0.59 | 0.19 | 0.40 | 3.31E-04 |
| cg08879910 | 6 | HLA-J | Body | Yes | 0.72 | 0.32 | 0.40 | 3.36E-04 |
| cg14936968 | 3 | IL17RD | Body | Yes | 0.69 | 0.26 | 0.43 | 3.36E-04 |
| cg08498787 | 11 | – | – | Yes | 0.66 | 0.25 | 0.41 | 3.36E-04 |
| cg15026277 | 17 | TMEM106A | TSS200 | Yes | 0.60 | 0.18 | 0.43 | 3.36E-04 |
| cg07519235 | 16 | GPRC5B | 5'UTR | Yes | 0.75 | 0.32 | 0.43 | 3.36E-04 |
| cg26388816 | 12 | B4GALNT3 | Body | Yes | 0.70 | 0.28 | 0.42 | 3.41E-04 |
| cg24033558 | 15 | SHF | Body | Yes | 0.68 | 0.27 | 0.41 | 3.42E-04 |
| cg01030534 | 7 | FAM115A | 5'UTR | No | 0.72 | 0.32 | 0.41 | 3.52E-04 |
| cg18726691 | 15 | RHCG | Exon 1 | Yes | 0.71 | 0.29 | 0.42 | 3.65E-04 |
| cg21211480 | 17 | TMEM106A | TSS200 | Yes | 0.59 | 0.18 | 0.41 | 3.71E-04 |
| cg14142965 | 12 | TXNRD1 | TSS200 | Yes | 0.62 | 0.19 | 0.43 | 3.88E-04 |
| cg14117138 | 19 | HIF3A | TSS1500 | Yes | 0.72 | 0.31 | 0.41 | 4.34E-04 |
| cg03514404 | 7 | FAM115A | 5'UTR | No | 0.70 | 0.29 | 0.41 | 4.67E-04 |
| cg02636041 | 10 | RASGEF1A | Body | Yes | 0.76 | 0.30 | 0.46 | 4.86E-04 |
| cg02245020 | 7 | FAM115A | 5'UTR | No | 0.69 | 0.28 | 0.40 | 5.28E-04 |
| cg16876647 | 2 | ZFP36L2 | Body | Yes | 0.62 | 0.22 | 0.40 | 8.57E-04 |
Abbreviations: TSS1500, 200 to 1500 base pairs upstream of the transcription start site; TSS200, 200 base pairs upstream of the transcription start site; UTR, untranslated region
a
The table shows differentially methylated CpGs (FDR Q-value <0.001) in PCa versus adjacent benign tissue that have a mean methylation (β-value) difference of at least 40%. All CpGs were hypermethylated in PCa; no hypomethylated CpGs were identified using the same selection criteria.