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Table 2 Differential methylation in individual biomarkers

From: High performance methylated DNA markers for detection of colon adenocarcinoma

Tissue

TMEFF2

GPX7

MAL

ARHGEF7

TWIST1

Ca

No

Ca

No

Ca

No

Ca

No

Ca

No

Number of samples

30

23

30

23

30

23

30

23

30

23

%M per sample

 Minimum

0

0

0

0

9

0

0

0

6

1

 25th percentile

40

0

1

0

21

1

0

0

14

3

 Median

59

1

33

0

33

2

8

0

18

4

 75th percentile

75

3

53

0

49

3

33

0

28

6

 Maximum

94

11

72

2

71

7

75

2

50

11

P value (Ca. vs. No.)

< 0.0001

< 0.0001

< 0.0001

< 0.0001

< 0.0001

Tissue

AKR1B1

HIN1

GAS7C

TM6SF1

ZNF671

Ca

No

Ca

No

Ca

No

Ca

No

Ca

No

Number of samples

30

23

30

23

30

23

30

23

30

23

%M per sample

 Minimum

0

0

0

0

0

0

0

1

0

2

 25th percentile

1

0

0

0

6

0

35

5

25

7

 Median

16

0

5

0

9

1

47

10

39

13

 75th percentile

21

0

18

0

12

2

58

15

49

16

 Maximum

52

1

61

0

36

4

70

40

72

20

P value (Ca. vs. No.)

< 0.0001

< 0.0001

< 0.0001

< 0.0001

< 0.0001

Tissue

COL6A2

APC

HIST1H3C

Ca

No

Ca

No

Ca

No

Number of samples

30

23

30

23

30

23

%M

 Minimum

0

1

0

0

0

0

 25th percentile

12

4

0

1

0

0

 Median

34

8

0

2

1

1

 75th percentile

52

10

58

2

55

3

 Maximum

66

23

92

7

78

8

P value (Ca. vs. No.)

< 0.0001

0.2662

0.3959

  1. Ca, Carcinoma; No, adjacent normal tissue; P value for Mann–Whitney test
  2. Methylation levels of 13 individual markers in colon carcinoma lesions – Descriptive Statistics. Fresh frozen tissues in the Training set were assayed for DNA methylation by QM-MSP. Non-parametric analyses of carcinoma (Ca) and adjacent normal (No) tissues indicated the percentiles of methylation and extent of differential methylation (Mann-Whitney P-value) between tissue types. TM6SF1, ZNF671, COL6A2 showed the highest background in adjacent normal colon tissues as observed at the 75th percentile. The other genes were ranked by percent methylation (%M) at the 75th percentile among carcinoma samples: TMEFF2 > GPX7 > MAL > ARHGEF7 > TWIST1 > AKR1B1 > HIN1 > GAS7. Additional file 1: Fig. S1 and Additional file 2: Table S1 show the box whiskers plots and performance analyses for these data