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Table 5 Representative enriched GO categories and pathways in mRNA association modules

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

index

drivers/regulators

N 1

function

p-value

44

ZIC1,MITF seg 18 CNV (+)

118

melanosome

1.300 × 10-7

45

TBP,MYB,HDAC2 seg 31 CNV (+)

77

RNA polymerase II regulation

1.35 × 10-5

45

TBP,MYB,HDAC2 seg 31 CNV (+)

77

condensed chromosome

7.928 × 10-5

46

SREBF2,EP300 seg 84 CNV (+)

49

cholesterol biosynthesis

3.781 × 10-4

47

E2F3,NFYA,SRF seg 30 CNV (+)

31

ceramide signaling pathway

4.302 × 10-5

47

E2F3,NFYA,SRF seg 30 CNV (+)

31

NFKB signaling pathway

8.632 × 10-4

48

TCF7L2 seg 42 CNV (+)

30

multi-drug resistance factors

5.884 × 10-5

48

TCF7L2 seg 42 CNV (+)

30

positive regulation of epithelial cell proliferation

1.096 × 10-4

49

NR2C1,NFYB seg 49 CNV (+)

22

mRNA translation

2.314 × 10-4

54

UBP1 seg 16 CNV (+)

18

RNA Pol II phosphorylation

4.429 × 10-4

56

APEX1 seg 57 (+)

16

cleavage of growing transcript

7.872 × 10-4

57

RPA2,EIF2C1 seg 16 CNV (+)

15

mRNA splicing

1.945 × 10-6

57

RPA2,EIF2C1 seg 16 CNV (+)

15

mRNA Pol II transcription initiation

7.260 × 10-4

59

RICS seg 51 CNV (+)

14

regulation of apoptosis

1.397 × 10-4

62

APC mutation (+)

136

liver development

4.932 × 10-4

66

TP53 mutation (-)

35

caspase activation

1.101 × 10-3

66

TP53 mutation (-)

35

P53 signaling pathway

4.138 × 10-4

68

TP53 mutation (+)

33

cell cycle

9.787 × 10-4

69

CDKN2A mutation (+)

32

cell motility

8.510 × 10-4

70

KRAS mutation (+)

25

DNA replication

2.689 × 10-3

71

PTEN mutation (+)

20

JNK cascade

2.904 × 10-4

75

PTEN mutation (-)

13

positive regulation of I-κB kinase/NF-κB cascade

1.745 × 10-3

79

CCND1,PPARG methylation (-)

13

negative regulation of cell proliferation

6.074 × 10-3

81

mir group 1 (-)

121

transport vesicle

3.297 × 10-4

82

mir group 2 (-)

121

translation

3.694 × 10-4

83

TF group 1 (+)

338

integrin signaling pathway

4.664 × 10-8

83

TF group 1 (+)

338

TGFβ signaling pathway

9.555 × 10-4

84

TF group 2 (+)

338

T cell differentiation

1.128 × 10-4

  1. Index: module index. N1: number of passengers in the module. Function: enriched GO category or pathway. p-value: hyper-geometric p-value for enrichment. Mir group 1 consists of mir-92,mir-96,mir-106a,mir 20b,mir-17,mir-19b,mir-32,mir-135,mir-25,mir-106b,mir-93,mir-106,mir-18,mir-20. Mir group 2 consists of mir-24,mir-99b,mir-27b,mir-21,mir-125a,mir-23b,mir-27a,mir-23a. TF group 1 consists of SMAD3,FOXD1,PLAU,BDNF,FOSL2,FOSL1,RBMS. TF group 2 consists of ERG,ELK4,NFATC1,POU5F1,ZNF350.
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BMC Systems Biology

ISSN: 1752-0509

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