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Table 4 Differential APC methylation, odds ratio, area under the curve (AUC) between adenocarcinoma, squamous cell carcinoma and their counterparts

From: Quantitative assessment of the diagnostic role of APC promoter methylation in non-small cell lung cancer

 

Adenocarcinoma

Squamous Cell Carcinoma

CpG site

MCaM (N = 535)

MCoM (N = 56)

P-valuea

FDRa

ORb

P-valueb

95% CIb

AUCb

MCaM (N = 386)

MCoM (N = 70)

P-valuea

FDRa

ORb

P-valueb

95% CIb

AUC†

cg15020645

0.26(40.7%)

0.13(0%)

3.5 × 10-32

1.0 × 10 -31

190.6

7.7 × 10 -6

22.65 to 2,321

0.72

0.13(14.77%)

0.11(0%)

0.087466

0.131199

3.16

0.406

0.28 to 68.72

0.61

cg16970232

0.3(45.2%)

0.11(0%)

5.0 × 10-38

3.0 × 10 -37

108.9

5.1 × 10 -6

17.64 to 1,043

0.73

0.15(18.91%)

0.09(0%)

2.7 × 10-7

1.6 × 10 -6

7.54

0.035

1.39 to 64.07

0.45

cg20311501

0.33(48.4%)

0.16(5.3%)

1.4 × 10-22

2.1 × 10 -22

61.56

4.96 × 10 -6

11.94 to 420

0.73

0.18(19.95%)

0.14(0%)

0.001955

0.003909

2.48

0.257

0.57 to 13.74

0.49

cg21634602

0.33(47.4%)

0.16(7.1%)

3.6 × 10-17

4.3 × 10 -17

23.34

3.6 × 10 -5

5.75 to 116.0

0.71

0.16(20.47%)

0.14(7.14%)

0.222306

0.266767

1.27

0.726

0.35 to 5.42

0.53

cg24332422

0.26(40.5%)

0.16(0%)

1.0 × 10-26

2.0 × 10 -26

223.6

2.81 × 10 -5

21.11 to 3,463

0.71

0.16(17.36%)

0.15(0%)

0.338755

0.338755

1.6

0.656

0.23 to 14.30

0.52

  1. MCaM, MCoM represent the mean of case methylation (Beta) and mean of control methylation (Beta). Methylation levels are calculated with formula: Beta = (M/M + U).
  2. aP-values are from t-test or Wilcoxon rank-sum test after false discovery rate (FDR adjustment). The t-test will be chose when the variable is normally distributed, or else the rank-sum test will be chose. Significant P-values after FDR are bolded which indicate significant different methylation between case and control.
  3. bOR and its 95% CI, P-value and AUC from logistic regression analysis or prediction model.