Table 3 Comparison of mean methylation between normal and tumor samples for the 17 genes studied with respect to the various clinicopathological parameters

ER+ (N = 27)

13^a, 14^b, 0^c

11, 15, 1

8, 16, 3

6, 21, 0

6, 20, 1

12, 15, 0

14, 11, 2

18, 9, 0

14, 13, 0

PERCENTAGE (%)

48^a, 52^b, 0^c

41, 56, 4

30, 59, 11

22, 78, 0

22, 74, 4

44, 56, 0

52, 41, 7

67, 33, 0

52, 48, 0

P ^a

0.857

0.741

0.137

0.007

0.004

0.791

0.115

0.095

0.81

P ^b

0.911

1.050

0.388

0.060

0.068

0.961

0.391

0.404

0.918

ER- (N = 30)

11, 14, 5

23, 7, 0

10, 20, 0

12, 18, 0

4, 26, 0

10, 18, 2

17, 13, 0

10, 20, 0

11, 19, 0

PERCENTAGE (%)

37, 47, 17

77, 23, 0

33, 67, 0

40, 60, 0

13, 87, 0

33, 60, 7

57, 43, 0

33, 67, 0

37, 63, 0

P ^a

0.228

0.001

0.010

0.013

0.00007

0.057

0.41

0.026

0.053

P ^b

0.298

0.009

0.057

0.055

0.001

0.108

0.498

0.074

0.113

PR+ (N = 24)

11, 13, 0

8, 15, 1

7, 16, 1

6, 18, 0

6, 18, 0

11, 13, 0

13, 9, 2

16, 8, 0

11, 13, 0

PERCENTAGE (%)

46, 54, 0

33, 63, 4

29, 67, 4

25, 75, 0

25, 75, 0

46, 54, 0

54, 38, 8

67, 33, 0

46, 54, 0

P ^a

0.989

0.196

0.063

0.015

0.001

0.977

0.123

0.157

0.310

P ^b

0.989

0.370

0.268

0.128

0.017

1.038

0.418

0.445

0.479

PR- (N = 33)

13, 15, 5

26, 7, 0

11, 20, 2

12, 21, 0

4, 28, 1

11, 20, 2

18, 15, 0

12, 21, 0

14, 19, 0

PERCENTAGE (%)

39, 45, 15

79, 21, 0

33, 61, 6

36, 64, 0

12, 85, 3

33, 61, 6

55, 45, 0

36, 64, 0

42, 58, 0

P ^a

0.36

0.0002

0.019

0.004

0.00003

0.082

0.325

0.098

0.180

P ^b

0.437

0.002

0.081

0.023

0.001

0.232

0.425

0.238

0.306

NODE- (N = 40)

19, 20, 1

20, 18, 2

11, 27, 2

15, 25, 0

6, 33, 1

18, 21, 1

25, 14, 1

20, 19, 1

15, 25, 0

PERCENTAGE (%)

48, 50, 3

50, 45, 5

28, 68, 5

38, 63, 0

15, 83, 3

45, 53, 3

63, 35, 3

50, 48, 3

36, 63, 0

P ^a

0.828

0.162

0.011

0.003

0.00001

0.267

0.107

0.581

0.021

P ^b

0.828

0.275

0.062

0.026

0.0002

0.378

0.202

0.658

0.071

NODE+ (N = 41)

21, 16, 4

27, 14, 0

14, 25, 2

14, 27, 0

10, 30, 1

13, 26, 2

20, 19, 2

21, 20, 0

18, 23, 0

PERCENTAGE (%)

51, 39, 10

66, 34, 0

34, 61, 5

34, 66, 05

24, 73, 2

32, 63, 5

49, 46, 5

51, 49, 0

44, 56, 0

P ^a

0.276

0.017

0.039

0.001

0.00001

0.032

0.165

0.564

0.496

P ^b

0.469

0.072

0.095

0.006

0.0002

0.091

0.312

0.685

0.703

T1 + T2 (N = 59)

33, 23, 3

34, 23, 2

16, 40, 3

22, 37, 0

11, 47, 1

23, 34, 4

36, 20, 3

33, 26, 0

27, 32, 0

PERCENTAGE (%)

56, 39, 5

58, 39, 3

27, 68, 5

37, 63, 0

19, 80, 2

39, 58, 3

61, 34, 5

56, 44, 0

46, 54, 0

P ^a

0.185

0.011

0.002

0.001

0.0000001

0.068

0.007

0.213

0.077

P ^b

0.262

0.037

0.011

0.009

0.000002

0.116

0.030

0.279

0.119

T3+T4 (N = 22)

7, 13, 2

13, 9, 0

9, 12, 1

7, 15, 0

5, 16, 1

8, 13, 1

9, 13, 0

8, 13, 1

6, 16, 0

PERCENTAGE (%)

32, 59, 9

59, 41, 0

41, 55, 5

32, 68, 0

23, 73, 5

36, 59, 5

41, 59, 0

36, 59, 5

27, 73, 0

P ^a

0.321

0.495

0.204

0.002

0.001

0.217

0.884

0.073

0.194

P ^b

0.496

0.647

0.495

0.017

0.017

0.461

0.884

0.310

0.550

STAGE 1+2 (N = 51)

25, 23, 3

27, 22, 2

15, 34, 2

20, 31, 0

9, 42, 0

21, 28, 2

31, 18, 2

28, 23, 0

22, 29, 0

PERCENTAGE (%)

49, 45, 6

53, 43, 4

29, 67, 4

39, 61, 0

18, 82, 0

41, 55, 4

61, 35, 4

55, 45, 0

43, 57, 0

P ^a

0.692

0.032

0.011

0.003

0.000001

0.118

0.035

0.436

0.074

P ^b

0.692

0.078

0.062

0.026

0.00001

0.182

0.074

0.570

0.140

STAGE 3+4 (N = 30)

15, 13, 2

20, 10, 0

10, 18, 2

9, 21, 0

7, 21, 2

10, 19, 1

14, 15, 1

13, 16, 1

11, 19, 0

PERCENTAGE (%)

50, 43, 7

67, 33, 0

33, 60, 7

30, 70, 0

23, 70, 7

33, 63, 3

47, 50, 3

43, 53, 3

37, 63, 0

P ^a

0.576

0.181

0.041

0.001

0.0002

0.100

0.347

0.279

0.217

P ^b

0.653

0.513

0.174

0.009

0.003

0.340

0.492

0.527

0.527

GRADE 1+2 (N = 32)

11, 19, 2

13, 18, 1

11, 20, 1

10, 22, 0

7, 25, 0

15, 17, 0

17, 13, 2

14, 18, 0

15, 17, 0

PERCENTAGE (%)

34, 59, 6

41, 56, 3

34, 63, 35

31, 69, 0

22, 78, 0

47, 53, 0

53, 41, 6

44, 56, 0

47, 53, 0

P ^a

0.085

0.681

0.088

0.009

0.0002

0.793

0.153

0.575

0.278

P ^b

0.361

0.827

0.299

0.077

0.003

0.899

0.434

0.815

0.675

GRADE 3 (N = 25)

13, 9, 3

21, 4, 0

7, 16, 2

8, 17, 0

3, 21, 1

7, 16, 2

14, 11, 0

14, 11, 0

10, 15, 0

PERCENTAGE (%)

52, 36, 12

84, 16, 0

28, 64, 8

32, 68, 0

12, 84, 4

28, 64, 8

56, 44, 0

56, 44, 0

40, 60, 0

P ^a

0.353

0.0003

0.006

0.007

0.0001

0.100

0.313

0.893

0.187

P ^b

0.500

0.003

0.034

0.030

0.002

0.283

0.484

0.893

0.318

CLINICOPATHOLOGICAL PARAMETERS

ATM

TP53

BRCA1

BRCA2

CHEK2

TIP60

RNF8

H2AX

ER+ (N = 27)

16, 11, 0

14, 10, 3

10, 17, 0

9, 14, 4

13, 10, 4

12, 14, 1

18, 9, 0

13, 11, 3

PERCENTAGE (%)

59, 41, 0

52, 37, 11

37, 63, 0

33, 52, 15

48, 37, 15

44, 52, 4

67, 33, 0

48, 41, 11

P ^a

0.264

0.390

0.374

0.260

0.988

0.760

0.062

0.474

P ^b

0.561

0.663

0.706

0.631

0.988

0.994

0.351

0.733

ER- (N = 30)

12, 15, 3

8, 21, 1

14, 16, 0

7, 21, 2

14, 16, 0

16, 8, 6

17, 11, 2

11, 18, 1

PERCENTAGE (%)

40, 50, 10

27, 70, 3

47, 53, 0

23, 70, 7

47, 53, 0

53, 27, 20

57, 37, 7

37, 60, 3

P ^a

0.857

0.039

0.765

0.016

0.885

0.111

0.206

0.150

P ^b

0.911

0.095

0.867

0.054

0.885

0.189

0.292

0.232

PR+ (N = 24)

13, 11, 0

12, 9, 3

7, 17, 0

8, 13, 3

12, 10, 2

10, 12, 2

17, 7, 0

13, 9, 2

PERCENTAGE (%)

54, 46, 0

50, 38, 13

29, 71, 0

33, 54, 13

50, 42, 8

42, 50, 8

71, 29, 0

54, 38, 8

P ^a

0.658

0.519

0.174

0.192

0.974

0.858

0.039

0.298

P ^b

0.860

0.735

0.423

0.408

1.104

1.042

0.221

0.507

PR- (N = 33)

15, 15, 3

10, 22, 1

17, 16, 0

8, 22, 3

15, 16, 2

18, 10, 5

18, 13, 2

11, 20, 2

PERCENTAGE (%)

45, 45, 9

30, 67, 3

52, 48, 0

24, 67, 9

45, 48, 6

55, 30, 15

55, 39, 6

33, 61, 6

P ^a

0.53

0.120

0.907

0.023

0.814

0.230

0.243

0.141

P ^b

0.601

0.255

0.907

0.078

0.865

0.355

0.344

0.266

NODE- (N = 40)

22, 15, 3

13, 25, 2

14, 26, 0

14, 22, 4

18, 20, 2

14, 22, 4

22, 17, 1

13, 25, 2

PERCENTAGE (%)

55, 38, 8

33, 63, 5

35, 65, 0

35, 55, 10

45, 50, 5

35, 55, 10

55, 43, 3

33, 63, 5

P ^a

0.068

0.028

0.080

0.370

0.591

0.183

0.291

0.021

P ^b

0.165

0.079

0.170

0.449

0.628

0.283

0.381

0.089

NODE+ (N = 41)

21, 19, 1

19, 20, 2

20, 21, 0

10, 26, 5

17, 19, 5

27, 11, 3

24, 16, 1

17, 21, 3

PERCENTAGE (%)

51, 46, 2

46, 49, 5

49, 51

24, 63, 12

41, 46, 12

66, 27, 7

59, 39, 2

41, 51, 7

P ^a

0.973

0.553

0.979

0.001

0.465

0.031

0.120

0.942

P ^b

1.034

0.723

0.979

0.009

0.719

0.105

0.255

1.068

T1 + T2 (N = 59)

35, 21, 3

23, 33, 3

26, 33, 0

19, 36, 4

27, 28, 4

32, 24, 3

35, 23, 1

19, 37, 3

PERCENTAGE (%)

59, 36, 5

39, 56, 5

44, 56, 0

32, 61, 7

46, 47, 7

54, 41, 5

59, 39, 2

32, 63, 5

P ^a

0.013

0.407

0.694

0.056

0.639

0.276

0.037

0.040

P ^b

0.037

0.461

0.694

0.106

0.679

0.335

0.090

0.085

T3+T4 (N = 22)

8, 13, 1

9, 12, 1

8, 14, 0

5, 12, 5

8, 11, 3

9, 9, 4

11. 10, 1

11, 9, 2

PERCENTAGE (%)

36, 59, 1

41, 55, 5

36, 64, 0

23, 55, 23

36, 50, 14

41, 41, 18

50, 45, 5

50, 41, 9

P ^a

0.230

0.433

0.157

0.035

0.295

0.744

0.767

0.562

P ^b

0.434

0.613

0.534

0.198

0.502

0.843

0.815

0.682

STAGE 1+2 (N = 51)

31, 17, 3

20, 27, 4

21, 30, 0

18, 31, 2

23, 25, 3

25, 23, 3

32, 18, 1

17, 32, 2

PERCENTAGE (%)

61, 33, 6

39, 53, 8

41, 59, 0

35, 61, 4

45, 49, 6

49, 45, 6

63, 35, 2

33, 63, 4

P ^a

0.013

0.397

0.499

0.100

0.674

0.636

0.015

0.020

P ^b

0.055

0.562

0.606

0.170

0.716

0.721

0.051

0.057

STAGE 3+4 (N = 30)

12, 17, 1

12, 18, 0

13, 17, 0

6, 17, 7

12, 14, 4

16, 10, 4

14, 15, 1

13, 14, 3

PERCENTAGE (%)

40, 57, 3

40, 60, 0

43, 57, 0

20, 57, 23

40, 47, 13

53, 33, 13

47, 50, 3

43, 47, 10

P ^a

0.252

0.434

0.280

0.005

0.303

0.524

0.983

0.674

P ^b

0.536

0.568

0.476

0.028

0.468

0.636

0.983

0.716

GRADE 1+2 (N = 32)

13, 17, 2

14, 17, 1

11, 21, 0

9, 19, 4

13, 17, 2

14, 14, 4

17, 13, 2

16, 13, 3

PERCENTAGE (%)

41, 53, 6

44, 53, 3

34, 66, 0

28, 59, 13

41, 53, 6

44, 44, 13

53, 41, 6

50, 41, 9

P ^a

0.845

0.486

0.64

0.043

0.491

0.452

0.487

0.795

P ^b

0.845

0.918

0.837

0.244

0.759

0.961

0.828

0.845

GRADE 3 (N = 25)

15, 9, 1

8, 14, 3

13, 12, 0

7, 16, 2

14, 9, 2

14, 8, 3

18, 7, 0

8, 16,1

PERCENTAGE (%)

60, 36, 4

32, 56, 12

52, 48, 0

28, 64, 8

16, 76, 8

56, 32, 12

72, 28, 0

32, 64, 4

P ^a

0.141

0.494

0.686

0.114

0.523

0.648

0.010

0.121

P ^b

0.266

0.646

0.729

0.277

0.635

0.734

0.034

0.257