Skip to main content

Table 5 Patterns of target genes’ promoter regions methylation and expression changes by mutations of the overlapping driver genes across tumor types

From: A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

Overlapping driver

genes

∣Ti∣

∣Ei∣

∣Ti ∩ Ei∣

∣DM∣

∣DE∣

\( \frac{\mid DM\cap DE\mid }{\mid DE\mid } \) (%)

p(DM ∙ DE)

p(−−)

p(+−)

p(−+)

p(++)

p.methyl

p.exp

TP53

8

11

7

10389

10066

52

2.8e-32

1

9.7e-95

7.1e-65

1

0

0

PTEN

3

1

1

12259

10293

61

0.014

1

1e-15

1e-15

1

2.98e-10

0

RB1

2

3

1

9049

8062

46

0.0066

0.81

0.05

1e-15

1

0

0

PIK3CA

1

2

1

13933

5822

73

5e-12

1

1e-15

5.4e-05

1

1.93e-11

0

ARID1A

1

2

1

9487

8573

53

1e-15

0.98

1e-15

0.29

1

0

0

KRAS

1

4

1

15041

8427

73

1

1

7.5e-12

1

0.87

0

0

KMT2D

2

1

1

9802

8485

52

4.3e-14

1

1e-15

0.014

1

7.37e-10

0

NF1

2

1

1

10288

7435

53

9e-07

1

1e-15

1e-15

1

0

0

CTNNB1

2

1

1

7583

7591

37

0.64

1

1e-15

1

1

0

0

EGFR

1

2

1

13156

10606

66

0.0096

1

1e-15

1e-15

1

7.63e-07

0

HRAS

2

3

2

8758

6300

47

3.7e-19

0.97

7e-29

8.1e-20

1

0

0

BRAF

2

2

2

9120

10092

47

1.3e-06

0.96

1.3e-14

7e-29

1

0

9.99e-16

IDH1

2

2

2

10596

10134

55

6.6e-16

1

7e-29

7e-29

1

0

0

CIC

1

1

1

14066

12718

71

1.2e-08

1

1e-15

1e-15

1

0

0

NRAS

2

2

1

8413

10581

43

5.6e-06

1

1e-15

1e-15

1

0

0

RNF43

2

2

2

9978

9292

51

4.9e-08

1

3.9e-29

2e-14

1

0

0

ATRX

1

2

1

11646

12114

60

2.2e-16

1

1e-15

1e-15

1

0

0

ZBTB20

2

2

2

8415

6667

43

1.1e-10

0.94

8.6e-19

2.1e-09

1

0

0

NOTCH1

1

2

1

10225

7849

55

1e-15

1

1e-15

1e-15

1

0

0

CDH1

2

2

2

8634

8254

45

3.6e-16

1

1.1e-23

3.5e-26

1

0

0

KEAP1

1

1

1

10060

10030

50

0.4

1

1e-15

0.017

1

1.25e-12

0

SMARCA4

1

1

1

6118

6234

30

0.86

1

1e-15

0.93

1

1.11e-16

3.56e-11

KIT

1

1

1

15035

10164

74

0.87

1

4.4e-16

0.029

0.95

2.54e-09

1.07e-06

KMT2B

2

2

2

8066

6649

44

1.7e-24

1

7e-29

2.3e-24

1

0

0

NSD1

1

1

1

13052

8233

67

1.2e-10

0.55

1.9e-14

3.1e-10

1

NA

NA

  1. |DM|: number of differentially methylated genes averaged across Ti ∩ Ei tumor types;
  2. |DE|: number of differentially expressed genes averaged across Ti ∩ Ei tumor types;
  3. \( \frac{\mid DM\cap DE\mid }{\mid DE\mid } \) (%): percent of differentially methylated target genes out of differentially expressed target genes, averaged across tumor types Ti ∩ Ei
  4. p(DM ∙ DE): p-value testing if number of target genes that are differentially methylated and expression is larger than expected using a hypergeometric distribution combined across tumor types Ti ∩ Eiusing the Fisher’s method.
  5. p(−−), p(+−), p(−+), p(++): p-values that test if number of target genes with “--”,“+-”,“-+”,“++” pattern of methylation and expression changes is larger than expected a using hypergeometric distribution combined across tumor types using the Fisher’s method.
  6. p.methyl: median p-value from testing if the number of overlapping target genes that are differentially methylated by the mutation of the CDG between any pair of two tumor types is larger than expected using a hypergeometric distribution.
  7. p.exp: median p-value from testing if the number of overlapping target genes that are differentially expressed by the mutation of the CDG between any pair of two tumor types is larger than expected using a hypergeometric distribution.
Back to article page

BMC Medical Genomics

ISSN: 1755-8794

Contact us