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Table 2 24 loci identified by MLDA, PAM and SAM as differentially methylated candidates in the comparison between A2780 cisplatin sensitive and cisplatin multiple-selected resistant cell lines.

From: Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands

microarray ID

status

validation

MLDA rank*

PAM rank

SAM rank

CGI***

gene symbol**

GenBank Accession

Chromosome

66_G_6

hypermethylated

Yes

1

1

1

Yes

   

121_D_9

hypermethylated

Yes

2

5

6

Yes

CRABP1

NM_004378

15

39_E_1

hypermethylated

ND

3

2

2

No

   

122_D_9

hypermethylated

No

4

11

11

Yes

SOX12

NM_006943

20

123_D_9

hypermethylated

No

5

10

10

Yes

SOX12

NM_006943

20

51_H_8

hypermethylated

Yes

6

18

19

No

FEZF2

NM_018008

3

58_A_1

hypermethylated

ND

7

22

22

Yes

   

80_H_5

hypermethylated

ND

8

14

16

No

   

21_A_11

hypermethylated

Yes

9

17

18

Yes

NTN4

NM_021229

12

38_D_7

hypermethylated

Yes

11

23

24

Yes

AGBL2

NM_024783

11

40_E_1

hypermethylated

ND

12

19

17

No

   

18_A_7

hypermethylated

ND

13

20

20

No

EDIL3

NM_005711

5

55_F_8

hypermethylated

Yes

14

9

9

Yes

BC127881

BC127881

7

122_B_1

hypermethylated

ND

15

16

14

No

   

109_A_6

hypermethylated

No

18

12

13

Yes

   

41_D_9

hypermethylated

Yes

22

8

8

Yes

WNT1

NM_005430

12

42_D_9

hypermethylated

ND

23

4

4

No

   

119_A_6

hypermethylated

Yes

24

6

5

Yes

NR2E1

NM_003269

6

63_A_8

hypermethylated

ND

26

15

15

No

   

6_D_4

hypermethylated

Yes

31

3

3

Yes

LMX1A

NM_177398

1

17_H_9

hypermethylated

Yes

34

13

12

Yes

HRASLS3

NM_006290

6

5_D_4

hypermethylated

Yes

35

7

7

Yes

LMX1A

NM_177398

1

24_D_3

hypermethylated

Yes

75

24

23

Yes

SP5

NM_001003845

2

122_G_1

hypermethylated

ND

101

21

21

Yes

   
  1. ND: not done. Yes: validated. No: not validated
  2. MLDA rank*: the rank of standardised residuals to the robust regression line constructed by the averaged sensitive scores against averaged resistant scores
  3. Gene symbol**: only the gene of which transcription start site (TSS) is within 5 kb span of the loci
  4. CGI***: CpG island defined by Gardiner-Garden and Frommer [31].