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Table 1 List of the 14 CpG methylation signatures for LGG IDH mutant versus IDH WT 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 mutant

Average β in WT

β = (avg β in mutant−avg β in WT)

p value

FDR

Average β in mutant

Average β in WT

β = (avg β in mutant−avg β in WT)

p value

FDR

1

cg00976453

KCNB1

0.795

0.037

0.758

1.31E−27

1.67E−27

0.806

0.162

0.644

1.18E−19

1.38E−19

2

cg02423318

NA

0.860

0.096

0.764

9.56E−28

1.67E−27

0.876

0.167

0.709

7.35E−21

2.87E−20

3

cg03300177

GNAO1

0.841

0.063

0.777

9.78E−28

1.67E−27

0.839

0.171

0.667

1.47E−20

2.95E−20

4

cg05866411

FGFRL1

0.784

0.102

0.682

8.35E−28

1.67E−27

0.681

0.208

0.473

3.96E−20

5.54E−20

5

cg07355841

TPPP3

0.835

0.055

0.781

1.25E−27

1.67E−27

0.819

0.184

0.635

1.93E−20

3.38E−20

6

cg08231710

MMP23A

0.874

0.127

0.747

9.35E−28

1.67E−27

0.809

0.293

0.516

1.47E−18

1.58E−18

7

cg08442798

NA

0.772

0.023

0.749

8.35E−28

1.67E−27

0.824

0.090

0.734

5.43E−21

2.87E−20

8

cg10064339

UCP2

0.779

0.042

0.737

8.35E−28

1.67E−27

0.805

0.115

0.690

8.82E−21

2.87E−20

9

cg10504751

GNAO1

0.846

0.067

0.779

1.23E−27

1.67E−27

0.846

0.173

0.673

2.61E−20

4.06E−20

10

cg11302533

NA

0.784

0.037

0.747

1.8E−27

1.94E−27

0.834

0.102

0.732

1.19E−20

2.87E−20

11

cg12565681

RHBDF2

0.834

0.053

0.781

1.44E−27

1.68E−27

0.822

0.295

0.527

5.87E−18

5.87E−18

12

cg20564913

FGFRL1

0.837

0.108

0.729

8.94E−28

1.67E−27

0.832

0.222

0.610

1.23E−20

2.87E−20

13

cg25499397

GPR62

0.822

0.076

0.746

8.35E−28

1.67E−27

0.798

0.272

0.527

1.12E−19

1.38E−19

14

cg25813864

RAPGEFL1

0.851

0.064

0.787

2.64E−27

2.64E−27

0.855

0.160

0.695

9.37E−21

2.87E−20

  1. NA not associated with any gene