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Table 2 The methylation status of the five CpG sites in the TCGA dataset and the validation dataset

From: Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC)

  CpG site Gene Position Relation to CpG_Island McaMb McoMb P valuec log10(OR)d 95% CId Sens Spec AUC
TCGA cg15830431 STK3 chr8:99952591 Island 0.28 0.09 2.20E−04 4.11 1.91–7.43 0.65 0.94 0.82
cg19396867 NAa chr19:40314862 N_Shore 0.45 0.20 3.60E−04 1.85 0.78–3.21 0.85 0.75 0.79
cg20655070 NAa chr19:40315011 Island 0.44 0.19 1.71E−03 1.61 0.67–2.72 0.64 0.88 0.75
cg26671652 ZNF418 chr19:58446312 N_Shore 0.35 0.16 5.77E−04 1.95 0.67–3.61 0.86 0.75 0.78
cg27062795 ZNF542 chr19:56879613 Island 0.43 0.17 3.60E−04 2.93 1.65–4.44 0.86 0.81 0.80
Validation cg15830431 STK3 chr8:99952591 Island 0.20 0.07 1.25E−06 3.04 1.82–4.53 0.66 0.77 0.71
cg19396867 NA chr19:40314862 N_Shore 0.37 0.12 2.71E−11 2.83 1.93–3.91 0.65 0.88 0.80
cg20655070 NA chr19:40315011 Island 0.31 0.09 8.04E−10 3.01 2.02–4.22 0.62 0.89 0.77
cg26671652 ZNF418 chr19:58446312 N_Shore 0.32 0.11 4.82E−11 3.20 2.18–4.39 0.58 0.93 0.79
cg27062795 ZNF542 chr19:56879613 Island 0.43 0.12 1.23E−12 2.55 1.77–3.50 0.72 0.82 0.83
  1. The sensitivity and specificity, as well as AUC, were both with a logistic regression prediction model without adjustment for gender, age, and smoking status and alcohol status
  2. Sens sensitivity, Spec specificity, AUC area under the curve
  3. aNA indicated that the CpG site is located outside of the coding region of the gene
  4. bMcaM represents the mean methylation percentage of the cases, and the McoM represents the mean methylation percentage of the controls
  5. c P value is calculated through the Wilcoxon rank-sum test followed by FDR (false discovery rate) adjustment for multiple correction
  6. dOR and 95% CI were determined by logistic regression