Table 2.
The hazard ratios and P-values for the associations between DNA methylation of seven key CpG loci and four clinical prognostic endpoints of GC patients in TCGA
| CpG sites | Genomic positions | Gene names | Genomic groups (CpG contents) | Training set | Validation set | Pooled set | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| HR (95% CI)a | P-value | FDR | HR (95% CI)a | P-value | HR (95% CI)a | P-value | ||||
| OS | ||||||||||
| cg11348188 | chr2–222,655,366 | EPHA4, PAX3 | Intergenic (open sea) | 1.69 (1.32–2.18) | 3.84 × 10−5 | 0.012 | 1.33 (1.05–1.68) | 0.017 | 1.46 (1.23–1.72) | 1.44 × 10− 5 |
| cg25117092a | chr3–150,948,274 | MED12L | Body (open sea) | 1.67 (1.29–2.16) | 1.03 × 10−4 | 0.017 | 1.28 (1.01–1.62) | 0.037 | 1.42 (1.20–1.69) | 4.70 × 10− 5 |
| cg05275153b | chr4–3,431,837 | RGS12 | Body (open sea) | 0.79 (0.68–0.91) | 9.97 × 10− 4 | 0.042 | 0.69 (0.56–0.86) | 8.99 × 10− 4 | 0.74 (0.65–0.84) | 3.02 × 10−6 |
| cg11671115 | chr10–87,336,486 | FAM190B, GRID1 | Intergenic (open sea) | 1.58 (1.22–2.04) | 4.85 × 10− 4 | 0.032 | 1.36 (1.08–1.71) | 0.010 | 1.42 (1.20–1.67) | 3.52 × 10−5 |
| cg14719951c | chr18–28,622,474 | DSC3 | Body (island) | 0.69 (0.55–0.87) | 1.33 × 10−3 | 0.048 | 0.74 (0.58–0.93) | 0.010 | 0.72 (0.61–0.84) | 4.22 × 10−5 |
| cg10399824d | chr10–121,048,354 | GRK5 | Body (open sea) | 0.61 (0.50–0.75) | 3.67 × 10−6 | 0.005 | 0.65 (0.53–0.80) | 4.01 × 10−5 | 0.65 (0.56–0.74) | 7.00 × 10−10 |
| cg24406668e | chr20–44,639,431 | MMP9 | Body (island) | 0.59 (0.46–0.76) | 2.88 × 10−5 | 0.011 | 0.78 (0.62–0.99) | 0.037 | 0.70 (0.59–0.82) | 2.29 × 10−5 |
| DSS | ||||||||||
| cg11348188 | chr2–222,655,366 | EPHA4, PAX3 | Intergenic (open sea) | 1.54 (1.16–2.06) | 3.10 × 10−3 | 0.028 | 2.05 (1.45–2.90) | 4.41 × 10−5 | 1.73 (1.39–2.15) | 9.42 × 10−7 |
| cg25117092a | chr3–150,948,274 | MED12L | Body (open sea) | 1.49 (1.10–2.00) | 8.95 × 10−3 | 0.043 | 1.75 (1.27–2.40) | 5.66 × 10−4 | 1.60 (1.29–1.98) | 2.17 × 10−5 |
| cg05275153b | chr4–3,431,837 | RGS12 | Body (open sea) | 0.67 (0.55–0.82) | 1.04 × 10−4 | 0.005 | 0.70 (0.53–0.91) | 0.009 | 0.69 (0.59–0.80) | 1.32 × 10−6 |
| cg11671115 | chr10–87,336,486 | FAM190B, GRID1 | Intergenic (open sea) | 1.59 (1.19–2.12) | 1.79 × 10−3 | 0.020 | 1.71 (1.26–2.31) | 5.65 × 10−4 | 1.65 (1.34–2.04) | 2.43 × 10−6 |
| cg14719951c | chr18–28,622,474 | DSC3 | Body (island) | 0.64 (0.49–0.85) | 1.62 × 10−3 | 0.020 | 0.65 (0.49–0.88) | 0.005 | 0.65 (0.53–0.79) | 2.16 × 10−5 |
| cg10399824d | chr10–121,048,354 | GRK5 | Body (open sea) | 0.54 (0.42–0.69) | 9.20 × 10−7 | 1.31 × 10−4 | 0.57 (0.44–0.73) | 7.12 × 10−6 | 0.57 (0.48–0.67) | 1.65 × 10−11 |
| cg24406668e | chr20–44,639,431 | MMP9 | Body (island) | 0.71 (0.53–0.93) | 1.46 × 10−2 | 0.050 | 0.54 (0.39–0.74) | 1.49 × 10− 4 | 0.62 (0.50–0.76) | 6.56 × 10−6 |
| PFI | ||||||||||
| cg11348188 | chr2–222,655,366 | EPHA4, PAX3 | Intergenic (open sea) | 1.65 (1.27–2.13) | 1.53 × 10−4 | 0.021 | 1.53 (1.17–1.99) | 0.002 | 1.58 (1.32–1.89) | 7.00 × 10−7 |
| cg25117092a | chr3–150,948,274 | MED12L | Body (open sea) | 1.47 (1.16–1.86) | 1.53 × 10−3 | 0.049 | 1.48 (1.12–1.94) | 0.005 | 1.49 (1.25–1.79) | 1.07 × 10−5 |
| cg05275153b | chr4–3,431,837 | RGS12 | Body (open sea) | 0.71 (0.59–0.87) | 6.84 × 10−4 | 0.043 | 0.54 (0.41–0.72) | 2.11 × 10−5 | 0.70 (0.61–0.80) | 2.17 × 10−7 |
| cg11671115 | chr10–87,336,486 | FAM190B, GRID1 | Intergenic (open sea) | 1.57 (1.24–1.99) | 1.86 × 10−4 | 0.021 | 1.40 (1.08–1.83) | 0.011 | 1.51 (1.27–1.80) | 3.12 × 10−6 |
| cg14719951c | chr18–28,622,474 | DSC3 | Body (island) | 0.69 (0.55–0.87) | 1.52 × 10−3 | 0.049 | 0.77 (0.60–0.99) | 0.043 | 0.73 (0.62–0.86) | 2.48 × 10−4 |
| cg10399824d | chr10–121,048,354 | GRK5 | Body (open sea) | 0.57 (0.46–0.7) | 1.26 × 10−7 | 5.62 × 10−5 | 0.75 (0.59–0.96) | 0.020 | 0.63 (0.54–0.74) | 5.10 × 10−9 |
| cg24406668e | chr20–44,639,431 | MMP9 | Body (island) | 0.68 (0.54–0.86) | 1.24 × 10−3 | 0.049 | 0.68 (0.52–0.90) | 0.007 | 0.69 (0.58–0.83) | 4.74 × 10−5 |
| DFI | ||||||||||
| cg11348188 | chr2–222,655,366 | EPHA4, PAX3 | Intergenic (open sea) | – | – | – | – | – | 1.51 (1.12–2.05) | 0.007 |
| cg25117092a | chr3–150,948,274 | MED12L | Body (open sea) | – | – | – | – | – | 1.75 (1.27–2.42) | 0.001 |
| cg05275153b | chr4–3,431,837 | RGS12 | Body (open sea) | – | – | – | – | – | 0.77 (0.63–0.94) | 0.012 |
| cg11671115 | chr10–87,336,486 | FAM190B, GRID1 | Intergenic (open sea) | – | – | – | – | – | 1.59 (1.18–2.14) | 0.002 |
| cg14719951c | chr18–28,622,474 | DSC3 | Body (island) | – | – | – | – | – | 0.74 (0.56–0.99) | 0.042 |
| cg103998244 | chr10–121,048,354 | GRK5 | Body (open sea) | – | – | – | – | – | 0.78 (0.60–1.01) | 0.059 |
| cg244066685 | chr20–44,639,431 | MMP9 | Body (island) | – | – | – | – | – | 0.77 (0.57–1.04) | 0.089 |
Abbreviations: GC gastric cancer, OS overall survival, DSS disease-specific survival, DFI disease-free interval, PFI progression-free interval, HRs hazard ratios, CI confidence interval, FDR false discovery rate
aCox regression analyses adjusting for age at initial pathologic diagnosis (continuous) and gender (male, female).
bDistance to the closest TSS for cg25117092 (MED12L) is 39,570 bp
cDistance to the closest TSS for cg05275153 (RGS12) is 2021 bp
dDistance to thee closest TSS for cg14719951 (DSC3) is 308 bp
eDistance to the closest TSS for cg10399824 is (GRK5) 81271 bp
fDistance to the closest TSS for cg24406668 is (MMP9) 1884 bp