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Table 1 Mutated driver genes per tumor

From: Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation

GBM sample

66

68

76

124

199

231

30

55

71

91

139

153

3

142

149

156

173

183

53

89

100

158

178

216

GBM subtype

IDH

MES

RTK1

RTK2

Coding mutation

SNVa

4

na

5

4

8

7

na

na

3

6

3

4

na

5

2

3

4

2

na

2

4

6

2

6

CNVb

-

na

-

-

2

-

na

na

1

1

-

-

3

1

2

-

-

-

1

1

1

1

1

-

Regulatory mutations

SNVc

na

na

na

-

-

na

na

na

-

na

na

 

na

na

-

1

na

na

na

-

-

na

na

na

CNVd

na

na

na

-

-

na

na

na

-

na

na

 

na

na

-

-

na

na

na

-

-

na

na

na

Methe

22

25

19

28

22

17

20

17

21

22

22

24

20

25

19

28

17

21

26

26

27

15

21

23

Meth. onlyf

20

25

19

27

17

16

20

17

20

19

22

23

19

24

18

27

17

21

25

23

26

13

19

23

  1. Tumors with 5 or more mutations are in bold
  2. na data not available
  3. -, not detected
  4. aCoding-sequence alternation
  5. bCoding-copy-number alternations
  6. cRegulatory-sequence alternation
  7. dRegulatory-copy-number alternations
  8. eNumbers of abnormally expressed (twofold or more expression differences from normal brain samples) driver genes for which methylation alternations describe their expression-variation
  9. fNumbers of abnormally expressed driver genes for which methylation alternations were the only type of mutation