Skip to main content

Table 1 Statistical analysis of differences in methylation levels between tumor and adjacent non-tumor tissues

From: Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer

 

Tumor

 

Adjacent Non-Tumor

   

Gene Name a

Methylation

Frequency b

Median

PMR c

Methylation

Frequency b

Median

PMR c

p-value d

MC

Corr. e

GDNF

95%

67.11

95%

3.29

5.0E-11

0.0017

MTHFR f

100%

56.51

100%

25.95

2.0E-10

*

OPCML g

95%

19.49

98%

5.80

1.0E-09

*

TNFRSF25

98%

50.52

93%

25.89

2.0E-07

*

TCF21

93%

60.64

88%

11.17

3.0E-07

*

PAX8 f

100%

83.90

100%

69.49

9.0E-06

0.0034

PTPRN2

80%

35.60

58%

4.02

1.0E-05

0.0052

PITX2

93%

19.37

95%

1.50

3.0E-05

0.0069

MT1G

95%

1.89

93%

0.59

0.0001

0.0086

PENK

93%

14.30

95%

6.82

0.0002

0.0103

GP1BB

98%

59.52

100%

42.68

0.0009

*

MGMT f

100%

26.73

98%

33.96

0.0009

*

SLC38A4 f

56%

6.00

31%

0.00

0.0010

0.0121

SFRP2

98%

10.19

91%

2.67

0.0038

*

RARRES1

60%

9.27

47%

0.71

0.0048

0.0138

DIRAS3

100%

57.25

100%

63.92

0.0074

*

NEUROG1

37%

3.03

17%

0.08

0.0079

0.0155

WDR33

31%

0.34

9%

0.20

0.0089

0.0172

TFAP2A

46%

5.68

20%

10.00

0.0092

0.0190

SFRP1

91%

1.63

98%

0.56

0.0124

*

CYP1B1

58%

3.53

40%

0.41

0.0143

*

HOXC9

66%

10.62

60%

0.48

0.0157

0.0207

ABCB1

100%

27.07

100%

24.33

0.0193

0.0224

HRAS f

100%

82.08

100%

90.01

0.0215

0.0241

GRIN2B

44%

28.03

31%

1.26

0.0235

0.0259

CACNA1G

93%

0.74

95%

0.44

0.0282

0.0276

HIC1

98%

33.81

100%

23.52

0.0315

0.0293

CPVL

66%

1.65

53%

0.33

0.0739

0.0310

SEZ6L

89%

5.08

95%

3.51

0.0745

0.0328

NEUROD1

44%

9.97

33%

0.70

0.0748

0.0345

CCND2

98%

1.74

96%

1.18

0.0827

0.0362

MINT1

98%

3.18

98%

2.49

0.0879

0.0379

DLEC

55%

19.39

64%

0.17

0.1169

*

RNR1

100%

43.28

100%

31.91

0.1930

0.0397

BLT1

98%

28.01

100%

25.63

0.2420

0.0414

ONECUT2

98%

17.23

100%

14.29

0.3369

*

PLAGL1

100%

45.72

100%

50.38

0.3747

0.0431

GATM

26%

11.95

69%

0.10

0.4462

0.0448

CDX1

98%

46.96

100%

44.40

0.7469

0.0466

TWIST1

66%

1.98

86%

1.07

0.7578

0.0483

TMEFF2

100%

11.54

100%

11.82

0.7591

*

RPA3

49%

0.24

49%

0.16

0.8863

0.0500

  1. a Human Genome Organization nomenclature. Loci showing a statistically significant difference in methylation between tumor and non-tumor tissue are highlighted in italics. The top eight loci are noted in bold. Loci are ranked in order of ascending p-value. b Percentage of samples with positive methylation value. c Median percent methylated reference calculated from positive methylation values. d p-value calculated by Wilcoxon signed rank test. e To minimize the risk of false discovery, a false-discovery rate threshold using the Benjamini and Hochberg (1995) approach was applied to all loci not previously found to be methylated in squamous cell lung cancer (see methods). f This reaction is not targeted to a CpG Island g This primer/probe set shares homology with the CpG island of the adjacent HNT gene, which appears to have arisen via gene duplication. * Denotes loci previously reported to be methylated in lung cancer tumor samples
Back to article page

Molecular Cancer

ISSN: 1476-4598