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Table 5 Methylation alterations in the CpG islands and the 5'-transitional CpG sites examined in gastric cancers containing high-level and low-level chromosomal losses

From: The 5'-end transitional CpGs between the CpG islands and retroelements are hypomethylated in association with loss of heterozygosity in gastric cancers

 

High-level chromosomal loss (n = 20)

Low-level chromosomal loss (n = 19)

 

Mean level of methylation

 

Methylation alterations (%)

Mean level of methylation

 

Methylation alterations (%)

CpG sites*

Normal

Tumor

p†

Hypo-

Hyper-

Normal

Tumor

p†

Hypo-

Hyper-

CpG islands

          

   CDH1, 0 kb

1.2

1.0

0.083

3 (15)

0 (0)

1.1

1.1

0.560

0 (0)

1 (5)

   RABGEF1, -0.2 kb

1.1

1.0

0.163

2 (10)

0 (0)

1.0

1.0

1

0 (0)

0 (0)

   STAG1, -0.4 kb

1.1

1.0

0.330

1 (5)

0 (0)

1.0

1.0

1

0 (0)

0 (0)

   MYBPC2, -0.6 kb

1.6

1.6

0.757

2 (10)

1 (5)

2.0

2.3

0.090

0 (0)

4 (21)

   MLH1, -0.6 kb

1.4

1.4

1

5 (25)

2 (10)

1.3

1.7

0.153

0 (0)

4 (21)

   PTEN, -0.9 kb

1.3

1.2

0.442

2 (10)

0 (0)

1.1

1.1

0.560

1 (5)

2 (11)

   CDKN2A, 0kb

1.1

1.0

0.330

1 (5)

0 (0)

1.0

1.4

0.072

0 (0)

4 (21)

   PAX5, -1.0 kb

2.0

1.7

0.115

7 (35)

0 (0)

1.9

2.1

0.505

4 (21)

5 (26)

   RUNX2, -3.8 kb

4.2

3.8

0.054

7 (35)

0 (0)

4.2

4.3

0.376

1 (5)

4 (21)

-3.0 kb

1.8

1.8

1

5 (25)

5 (25)

2.0

2.0

1

3 (16)

4 (21)

-0.7 kb

2.1

2.0

0.575

5 (25)

4 (20)

1.7

1.9

0.266

4 (21)

6 (32)

+1.6 kb

2.0

2.2

0.295

3 (15)

5 (25)

2.1

2.5

0.066

2 (11)

7 (37)

   RUNX3, -1.7 kb

2.0

3.3

<0.0001

0 (0)

14 (70)

2.5

3.3

0.012

0 (0)

12 (63)

-0.5 kb

1.3

1.1

0.121

6 (30)

2 (10)

1.8

2.4

0.035

2 (11)

9 (47)

-0.1 kb

1.2

1.0

0.042

4 (20)

0 (0)

1.0

1.2

0.042

0 (0)

4 (21)

+1.0 kb

4.0

3.8

0.519

6 (30)

5 (25)

3.4

3.8

0.012

0 (0)

7 (37)

   VDR, +0.1 kb

1.0

1.0

1

0 (0)

0 (0)

1.0

1.0

1

0 (0)

0 (0)

   KIAA1752, +0.4 kb

2.8

2.6

0.096

8 (40)

0 (0)

2.1

2.5

0.084

0 (0)

7 (37)

Transitional CpGs

          

   MYBPC2, -1.2 kb

4.3

4.1

0.083

4 (20)

0 (0)

4.3

4.2

0.546

5 (26)

2 (11)

   VDR, -0.7 kb

1.8

1.3

0.003

10 (50)

0 (0)

1.5

2.1

0.056

3 (16)

8 (42)

   ESR2, -0.9 kb

1.7

1.4

0.114

6 (30)

0 (0)

1.3

1.5

0.141

0 (0)

4 (22)

   MLH1, -1.0 kb

3.1

2.5

0.050

9 (45)

2 (10)

2.8

3.5

0.035

1 (5)

11 (58)

   FLJ43855, -1.1 kb

4.0

3.5

0.043

10 (50)

2 (10)

3.7

4.1

0.072

2 (11)

8 (42)

   PTEN, -1.4 kb

1.4

1.1

0.062

5 (25)

0 (0)

1.1

1.3

0.119

1 (5)

5 (26)

   CDKN2A, -1.5 kb

2.0

1.6

0.012

10 (50)

2 (10)

2.0

2.8

0.025

3 (16)

10 (53)

+0.8 kb

4.4

3.6

0.002

12 (60)

0 (0)

4.1

4.4

0.173

3 (16)

7 (37)

   MUC8, +2.0 kb

4.4

3.7

0.001

9 (45)

0 (0)

4.4

4.2

0.149

6 (32)

2 (11)

   MAGEA2, 0 kb

4.8

3.4

<0.0001

11 (55)

0 (0)

4.8

4.6

0.336

2 (11)

0 (0)

   DDX53, 0 kb

4.2

3.7

0.051

9 (45)

2 (10)

4.5

3.9

0.096

6 (32)

2 (11)

   TFF2, -0.2 kb

2.4

2.1

0.174

7 (35)

2 (10)

2.2

2.0

0.324

6 (32)

2 (11)

   SERPINB5, -0.3 kb

2.7

2.2

0.080

10 (50)

3 (15)

2.4

2.5

0.598

2 (11)

4 (21)

   MSLN, -0.8 kb

4.3

3.6

0.005

11 (55)

2 (10)

3.5

3.7

0.591

1 (5)

5 (26)

  1. *CpG sites are indicated by the name of the gene and the distance from the transcription start site.
  2. †p values were calculated by an independent t test for the mean values.
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BMC Cancer

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