Table 2 Top 20 SFEs in terms of differential frequencies in pooled CIMP+ vs . pooled CIMP− samples

MLH1.METHYLATION

0.100

38

0.107

4

0.01

7.11 × 10 ⁻¹³

3.40 × 10 ⁻¹⁰

MGMT.METHYLATION

0.113

58

0.163

29

0.05

2.22 × 10 ⁻⁰⁸

5.30 × 10 ⁻⁰⁶

MFN1.PIK3CA.TERC.GNB4.SOX2.MECOM.ZMAT3.KCNMB3.ZNF639.KCNMB2..chr3.168753729.181290583_AMP

−0.094

17

0.048

82

0.14

3.06 × 10 ⁻⁰⁶

4.89 × 10 ⁻⁰⁴

BRAF..BRAF_MUTATION

0.063

30

0.084

12

0.02

1.15 × 10 ⁻⁰⁵

1.38 × 10 ⁻⁰³

PTEN..PTEN_MUTATION

0.080

47

0.132

30

0.05

2.48 × 10 ⁻⁰⁵

2.38 × 10 ⁻⁰³

KRAS..KRAS_MUTATION

0.091

62

0.174

48

0.08

4.07 × 10 ⁻⁰⁵

3.25 × 10 ⁻⁰³

SETD2..SETD2_MUTATION

0.053

25

0.070

10

0.02

5.86 × 10 ⁻⁰⁵

4.01 × 10 ⁻⁰³

LOC148145.C19orf12.CCNE1..chr19.29379723.30313894_AMP

−0.044

3

0.008

30

0.05

2.02 × 10 ⁻⁰⁴

1.21 × 10 ⁻⁰²

CACNA1A.BRD4.NOTCH3..chr19.15367544.15380857_AMP

−0.035

1

0.003

22

0.04

2.98 × 10 ⁻⁰⁴

1.59 × 10 ⁻⁰²

PIK3R1..PIK3R1_MUTATION

0.046

25

0.070

14

0.02

1.10 × 10 ⁻⁰³

5.28 × 10 ⁻⁰²

DNM2..chr19.10877710.10887626_AMP

−0.024

0

0.000

14

0.02

1.46 × 10 ⁻⁰³

6.35 × 10 ⁻⁰²

PBRM1..PBRM1_MUTATION

0.058

43

0.121

36

0.06

2.37 × 10 ⁻⁰³

9.46 × 10 ⁻⁰²

ATM..ATM_MUTATION

0.042

25

0.070

16

0.03

2.82 × 10⁻⁰³

1.01 × 10⁻⁰¹

TP53..TP53_MUTATION

−0.101

143

0.402

290

0.50

2.94 × 10⁻⁰³

1.01 × 10⁻⁰¹

ARID1A..ARID1A_MUTATION

0.052

40

0.112

35

0.06

6.16 × 10⁻⁰³

1.95 × 10⁻⁰¹

GSTP1.METHYLATION

0.054

44

0.124

40

0.07

6.51 × 10⁻⁰³

1.95 × 10⁻⁰¹

SAMD4B..chr19.39837455.39850028_AMP

−0.024

2

0.006

17

0.03

1.47 × 10⁻⁰²

3.76 × 10⁻⁰¹

TMED11P.CTBP1.SPON2..chr4.1105313.1243877_DEL

−0.016

0

0.000

9

0.02

1.55 × 10⁻⁰²

3.76 × 10⁻⁰¹

KEAP1..KEAP1_MUTATION

−0.016

0

0.000

9

0.02

1.55 × 10⁻⁰²

3.76 × 10⁻⁰¹

FOSL2.PLB1..chr2.28628327.28860856_AMP

−0.017

0

0.000

10

0.02

1.65 × 10⁻⁰²

3.76 × 10⁻⁰¹