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
From: DNA methylation signatures associated with prognosis of gastric cancer
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 |