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Table 3 List of the 14 CpG methylation signatures for oligodendroglioma (ODG) versus diffuse astrocytoma (DA) in the training set and validation set (GSE58218)

From: DNA methylation signatures for 2016 WHO classification subtypes of diffuse gliomas

   

Training set (TCGA cohort)

Validation set (GSE58218 cohort)

No.

CpG ID

Gene name

Average β in ODG

Average β in DA

β = (avg β in ODG−avg β in DA)

p value

FDR

Average β in ODG

Average β in DA

β = (avg β in ODG−avg β in DA)

p value

FDR

1

cg00873351

CD300LB

0.755

0.227

0.528

1.67E−32

3.9E−32

0.576

0.225

0.351

1.92E−22

2.99E−22

2

cg03492827

NA

0.647

0.192

0.455

8.18E−34

5.73E−33

0.701

0.286

0.415

3.01E−26

2.11E−25

3

cg04437966

FLJ37543

0.500

0.088

0.412

3.99E−33

1.39E−32

0.459

0.102

0.357

2.33E−25

8.16E−25

4

cg07250222

FGFR2

0.753

0.186

0.567

8.68E−30

8.68E−30

0.795

0.301

0.494

5.03E−21

7.04E−21

5

cg07847030

TCF7L1

0.730

0.163

0.567

6.78E−31

1.06E−30

0.798

0.368

0.429

2.62E−19

2.62E−19

6

cg07893801

PLCG1

0.807

0.312

0.495

1.28E−32

3.59E−32

0.737

0.378

0.359

1.61E−20

2.04E−20

7

cg08935418

PTPRN2

0.735

0.231

0.505

6.25E−30

6.73E−30

0.771

0.313

0.458

4.01E−23

7.53E−23

8

cg09772154

FGFR2

0.733

0.194

0.540

5.94E−30

6.73E−30

0.779

0.308

0.472

6.35E−20

6.84E−20

9

cg10363569

PRKAG2

0.675

0.162

0.513

5.1E−30

6.5E−30

0.574

0.196

0.377

5.22E−20

6.09E−20

10

cg12210255

NA

0.662

0.139

0.523

2.53E−33

1.18E−32

0.699

0.237

0.462

1.8E−24

5.05E−24

11

cg13412754

MAPKAP1

0.782

0.311

0.471

4.67E−32

9.34E−32

0.736

0.340

0.396

1.74E−25

8.1E−25

12

cg13598010

NA

0.778

0.175

0.603

1.89E−34

2.65E−33

0.790

0.254

0.536

5.09E−27

7.13E−26

13

cg19093820

GPR156

0.210

0.716

−0.506

3.56E−31

6.23E−31

0.211

0.655

−0.444

4.3E−23

7.53E−23

14

cg23759393

PTPRN2

0.722

0.203

0.518

1.08E−30

1.51E−30

0.790

0.300

0.490

8.76E−24

2.04E−23

  1. NA not associated with any gene