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Table 2 The averages of the number of estimated edges, the five performance measures and the computation time (sec.) over 50 datasets

From: Enhanced construction of gene regulatory networks using hub gene information

p

n

Method

\(|\hat {E}|\)

SEN

SPE

FDR

MISR

MCC

Time

83

41

GeneNet

6.04

5.32

99.98

6.57

2.88

19.21

0.05

(|E|=103)

  

(0.61)

(0.52)

(0.00)

(1.64)

(0.01)

(1.46)

(0.00)

  

NS

2.36

2.21

100.00

2.83

2.96

13.29

0.09

   

(0.20)

(0.19)

(0.00)

(1.42)

(0.01)

(0.82)

(0.01)

  

SPACE

4.62

4.04

99.99

6.41

2.92

16.18

0.03

   

(0.79)

(0.64)

(0.00)

(2.36)

(0.02)

(1.40)

(0.00)

  

ESPACE

7.28

6.37

99.98

5.75

2.86

21.04

0.01

   

(0.94)

(0.78)

(0.01)

(1.38)

(0.02)

(1.55)

(0.00)

  

GLASSO

11.40

8.78

99.93

16.81

2.83

25.48

0.00

   

(0.87)

(0.59)

(0.01)

(2.05)

(0.01)

(0.88)

(0.00)

  

GLASSO-SF

9.90

7.53

99.94

16.30

2.86

23.44

0.12

   

(0.81)

(0.53)

(0.01)

(2.08)

(0.01)

(0.84)

(0.00)

  

EGLASSO

11.28

8.89

99.94

15.36

2.82

25.93

0.00

   

(0.86)

(0.59)

(0.01)

(1.86)

(0.01)

(0.88)

(0.00)

  

PCACMI

48.44

27.24

99.38

41.86

2.80

38.52

0.54

   

(0.82)

(0.55)

(0.02)

(1.00)

(0.03)

(0.68)

(0.01)

  

CMI2NI

48.72

27.88

99.39

40.82

2.77

39.35

0.54

   

(0.85)

(0.55)

(0.02)

(0.96)

(0.03)

(0.65)

(0.01)

 

83

GeneNet

34.74

31.17

99.92

7.05

2.16

52.97

0.06

   

(0.83)

(0.61)

(0.01)

(0.74)

(0.02)

(0.50)

(0.00)

  

NS

15.14

14.52

99.99

1.07

2.59

37.20

0.15

   

(0.43)

(0.41)

(0.00)

(0.38)

(0.01)

(0.55)

(0.01)

  

SPACE

51.84

41.03

99.71

16.81

2.07

56.67

0.05

   

(1.95)

(1.28)

(0.02)

(1.06)

(0.03)

(1.11)

(0.00)

  

ESPACE

52.34

42.45

99.74

15.42

2.00

58.82

0.03

   

(1.46)

(0.86)

(0.02)

(0.96)

(0.02)

(0.54)

(0.00)

  

GLASSO

27.98

23.24

99.88

12.57

2.44

43.63

0.00

   

(1.33)

(0.96)

(0.02)

(1.32)

(0.03)

(0.97)

(0.00)

  

GLASSO-SF

28.04

22.82

99.86

14.53

2.47

42.86

0.13

   

(1.31)

(0.90)

(0.02)

(1.41)

(0.02)

(0.89)

(0.00)

  

EGLASSO

30.06

26.17

99.91

8.91

2.33

47.48

0.00

   

(1.33)

(1.03)

(0.01)

(1.15)

(0.03)

(1.01)

(0.00)

  

PCACMI

28.44

25.96

99.95

6.09

2.29

48.66

0.56

   

(0.44)

(0.49)

(0.01)

(0.79)

(0.02)

(0.61)

(0.00)

  

CMI2NI

28.66

26.76

99.97

3.85

2.25

50.02

0.54

   

(0.45)

(0.46)

(0.01)

(0.61)

(0.02)

(0.53)

(0.01)

  1. The reported values for the SEN, SPE, FDR, MISR and MCC were multiplied by 100. Numbers in the parentheses denote the standard errors
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