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Table 3 Summary of topological and biological analysis of gene module and their corresponding protein modules for Set 1

From: Two-layer modular analysis of gene and protein networks in breast cancer

Module Id

1

2

3

4

5

6

7

#U Sum

Topological analysis

        

Genes

142

142

125

40

35

22

7

513

Expressed proteins

640

486

439

159

152

79

10

1958

PPI

7465

6576

8163

2106

1317

885

126

24752

Processed protein in PPI

3284

3206

3187

1338

797

575

114

6519

Processed PPI

6951

6095

7712

1985

1250

794

113

23173

α

1.606

1.632

1.576

1.701

1.658

1.698

1.777

 

Qmax

0.637

0.662

0.632

0.714

0.792

0.798

0.793

 

Modules (Isolated modules)

309 (7)

259 (4)

28 (11)

26 (10)

23 (8)

17 (7)

6 (4)

155 (51)

%age accuracy, LOO-CV

86.510

87.410

95.199

99.028

99.624

100

100

 

Avg. Qmax, LOO-CV

0.639

0.664

0.634

0.714

0.797

0.797

0.791

 

Module range, LOO-CV

24-33

20-28

24-34

25-32

21-25

16-18

5-6

 

Avg. Modules, LOO-CV

28

26

28

26

22

16

5

 

Biological analysis

        

GO:BP, Groups

137

135

111

71

45

34

6

539

GO:BP, Terms

96

117

96

67

47

37

8

205

GO:BP, Referenced

42

54

46

32

25

19

8

85

GO:MF, Groups

131

124

115

69

44

35

7

525

GO:MF, Terms

79

72

72

51

33

30

10

145

GO:MF, Referenced

55

40

43

34

24

23

8

91

GO:CC, Groups

112

95

92

55

42

32

6

434

GO:CC, Terms

15

14

14

11

10

13

6

23

GO:CC, Referenced

12

11

12

9

8

9

6

16

  1. Topological analysis represents the analysis of network topology, while biological analysis represents the domain analysis of individual modules; Genes, Number of genes; Expressed Proteins, Proteins expressed by genes in module; PPI, Number of interaction between proteins; Processed protein in PPI, Number of proteins after removing loops and multiple edges; Processed PPI, Number of interaction in processed PPI; α, Power law exponent; Qmax, maximum modularity score; LOO-CV, Leave-one-out cross-validation; Avg. modules, Mean number of modules in LOO-CV; GO:BP, GO:MF, GO:CC represent the GO biological process, GO molecular function, GO cellular component respectively, while Groups represents the domain groups annotated with each module, Terms represent the unique number of GO term; and Referenced represents GO terms previously reported in literature, #U Sum, Unique sum.