Skip to main content

Table 3 Mean percent methylation by gene and tissue type from the Breast Cancer Care in Chicago study

From: Exploring DNA methylation changes in promoter, intragenic, and intergenic regions as early and late events in breast cancer formation

DNA region

Controla

Adjacentb

Invasivec

Adjacent vs. control

Invasive vs. control

Invasive vs. adjacent

 

N

Mean

SD

N

Mean

SD

N

Mean

SD

Diff.

P-valued

Diff.

P-valued

Diff.

P-valuee

Promoter region

               

  BRCA1

15

1.6

1.1

105

1.4

4.3

105

3.0

9.6

-0.2

NS

1.4

NS

1.6

0.031

  CD44f

18

1.6

0.6

37

1.8

0.9

37

2.6

2.7

0.2

NS

1.0

NS

0.8

NS

  ESR1f

18

5.9

3.1

37

7.9

6.0

37

6.7

7.8

2.0

NS

0.8

NS

-1.2

NS

  GSTM2

16

1.8

2.0

107

3.0

6.1

107

19.3

22.9

1.2

NS

17.5

0.004

16.3

<0.0001

  GSTP1

17

2.5

2.0

118

1.6

3.7

118

9.9

16.8

-0.9

NS

7.4

NS

8.3

<0.0001

  MAGEA1f

17

84.8

4.9

32

84.2

4.8

37

67.0

16.2

-0.6

NS

-17.8

0.0001

-17.2

<0.0001

  MSI1f

18

3.8

2.1

36

4.2

2.5

37

9.2

7.4

0.4

NS

5.3

0.0001

5.0

0.0003

  NFE2L3f

17

28.9

14.7

36

26.9

13.7

37

33.7

24.4

-2.0

NS

4.8

NS

6.8

NS

  RASSF1A

18

2.8

2.2

124

9.7

10.7

124

33.3

23.4

6.9

<0.0001

30.5

<0.0001

23.6

<0.0001

  RUNX3

17

3.3

1.2

119

4.0

3.3

119

11.4

12.7

0.7

NS

8.1

0.061

7.4

<0.0001

  SIX3

17

5.8

2.8

115

5.3

4.0

115

15.7

14.9

-0.5

NS

9.9

0.026

10.4

<0.0001

  TFF1

18

81.8

5.4

122

72.0

16.9

122

49.2

22.3

-9.8

0.008

-32.6

<0.0001

-22.8

<0.0001

Upstream of promoter

               

  EN1

18

17.8

5.3

122

20.0

10.2

122

32.9

15.3

2.2

NS

15.1

<0.0001

12.9

<0.0001

  PAX3

17

2.9

1.2

121

4.0

5.2

121

10.8

11.1

1.1

NS

7.9

0.0003

6.8

<0.0001

  PITX2f

17

26.5

6.1

35

27.6

8.6

36

36.1

11.3

1.1

NS

9.6

0.001

8.5

<0.0001

  SGK1

18

1.6

1.2

124

3.9

3.7

124

13.0

12.2

2.3

<0.0001

11.4

<0.0001

9.1

<0.0001

Introns

               

  APC

18

2.0

1.9

114

2.9

8.3

114

14.8

19.6

0.9

NS

12.8

0.058

11.9

<0.0001

  EGFR

18

4.5

1.3

126

7.3

5.2

126

19.4

14.8

2.8

0.006

14.9

<0.0001

12.1

<0.0001

  LHX2f

18

21.1

5.3

36

25.8

13.1

37

36.1

12.6

4.7

NS

15.0

<0.0001

10.3

0.0007

  RFX1

18

18.0

5.3

126

19.3

9.7

126

39.4

13.1

1.3

NS

21.4

<0.0001

20.1

<0.0001

  SOX9

18

8.4

4.3

123

9.1

7.4

123

15.2

14.3

0.7

NS

6.8

NS

6.1

0.002

DNA Repeats

               

  LINE-1

18

68.7

1.4

129

72.8

2.6

129

71.2

4.3

4.1

<0.0001

2.5

0.0003

-1.6

0.001

  Sat2

18

52.6

8.0

128

57.4

12.7

128

52.0

13.4

4.8

0.002

-0.6

NS

-5.4

<0.0001

  1. aReduction mammoplasty samples from women unaffected with breast cancer
  2. bSamples from histologically normal tissue adjacent to the tumor
  3. cSamples from the cancer component of the tumor
  4. dFrom an independent sample Wilcoxon Rank Sum test comparing control mammoplasty vs. adjacent samples
  5. eFrom a dependent sample Wilcoxon Sign Rank test. P-values > 0.10 are suppressed. Diff, difference in mean methylation; SD, standard deviation
  6. fThese seven assays were not pursued beyond the pilot phase and, therefore, had 32-37 paired cancer and adjacent samples instead of 105-129
  7. Differences were determined to be statistically significant at p < 0.001 for the complete sample set and p < 0.01 for regions only examined in the pilot study
Back to article page

BMC Cancer

ISSN: 1471-2407

Contact us