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Table 2 Network enrichment analysis of lung cancer-related gene sets to patient-specific altered gene sets

From: Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

Functional gene set

FNEA (kā€‰=ā€‰ 100)

MNEA

GEA (kā€‰=ā€‰ 100)

GSEA

Ding et al., 2008

    

ā€ƒAll (623 genes)

66

114

1

102

ā€ƒDrivers (26)

74

95

21

16

ā€ƒMutated ā‰¤1 (153)

39

102

2

75

COSMIC

    

ā€ƒDetected >1 (110)

34

33

22

30

ā€ƒDetected once (median)āˆ— (110)

18

52

9

28.5

KEGG05223 non-small cell lung cancer (56)

48

99

2

40

Largest contrast GEA > FNEA

    

ā€ƒKEGG00362 Benzoate degradation via hydroxylation (3)

4

27

123

31

ā€ƒKEGG00513 High-mannose type N-glycan biosynthesis (4)

2

5

123

24

ā€ƒKEGG00780 Biotin metabolism (4)

1

13

123

11

ā€ƒKEGG00300 Lysine biosynthesis (5)

0

6

123

34

ā€ƒKEGG00785 Lipoic acid metabolism (4)

0

2

123

18

Largest contrast FNEA > GEA

    

ā€ƒGO0001666 Response to hypoxia (163)

119

114

11

105

ā€ƒKEGG05200 Pathways in cancer (254)

112

118

6

99

ā€ƒGO0001525 Angiogenesis (129)

115

113

10

118

ā€ƒKEGG04010 MAPK signaling pathway (286)

107

114

4

82

ā€ƒKEGG04020 Calcium signaling pathway (183)

99

108

5

60

  1. KEGG05223 is non-small cell lung cancer pathway. ā€˜COSMICā€™ genes include the lung-cancer somatic mutations in the COSMIC database, but exclude those in [26]. āˆ— indicates the median from 50 randomly sampled sets.