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Table 4 Summary of co-citations in mRNA and microRNA association modules

From: Deciphering causal and statistical relations of molecular aberrations and gene expressions in NCI-60 cell lines

mRNA modules

    

index

drivers/regulators

N 1

N 2

N 3

44

ZIC1,MITF seg 18 CNV (+)

118

14

6

45

TBP,MYB,HDAC2 seg 31 CNV (+)

77

28

20

46

SREBF2,EP300 seg 84 CNV (+)

49

3

2

47

E2F3,NFYA,SRF seg 30 CNV (+)

31

5

4

48

TCF7L2 seg 42 CNV (+)

30

1

3

54

UBP1 seg 16 CNV (+)

18

1

0

62

APC mutation (+)

136

17

10

63

APC mutation (-)

56

3

6

65

CDNK2A mutation (-)

43

3

6

66

TP53 mutation (-)

35

11

3

67

BRAF mutation (-)

34

3

3

68

TP53 mutation (+)

33

4

6

69

CDKN2A mutation (+)

32

6

3

71

PTEN mutation (+)

20

1

2

72

KRAS mutation (-)

16

1

1

73

BRAF mutation (+)

16

3

1

75

PTEN mutation (-)

13

2

4

76

PAX8 methylation (-)

67

1

4

77

BCR methylation (-)

58

5

10

79

CCND1,PPARG methylation (-)

13

4

7

80

COL5A1 methylation (-)

10

1

1

83

TF group 1 (+)

338

236

48

microRNA modules

    

index

drivers/regulators

N1

N2

N3

4

ZIC1,MITF seg 18 CNV (-)

19

3

5

5

DNMT1 seg 15 CNV (+)

15

1

2

6

SRF seg 30 CNV (+)

13

1

1

7

MAP2K4 seg 66 CNV (-)

13

2

2

10

TP53 mutation (+)

17

3

3

12

APC mutation (+)

10

1

1

14

BCR methylation (-)

12

1

4

15

SMAD3,BDNF (+)

28

8

10

20

HIF1A (+)

14

1

2

  1. Index: module index. N1: number of passengers in the module. N2: number of co-cited driver/regulator-passenger pairs in the module. N3: max number of co-cited driver/regulator-passengers over 10 random modules of the same size. TF group 1 consists of SMAD3,FOXD1,PLAU,BDNF,FOSL2,FOSL1,RBMS. TF group 2 consists of ERG,ELK4,NFATC1,POU5F1,ZNF350.