Table 2 Comparison of CASCADE to competing clustering methods for 2 biological network data sets (BIOGRID Yeast PPI network, DIP Yeast PPI network).

Number

(%)

Function

Location

Complex

mf

cc

bp

BIOGRID Yeast PPI network

CASCADE

225

19.6

18.3

3.26

2.55

5.13

4.67

4.24

3.53

STM

248

18.1

16.2

2.88

2.37

4.64

4.17

3.98

3.53

Maximal clique

587

3.6

80.8

2.71

2.21

4.53

3.55

3.47

2.99

Quasi clique

431

7.4

40.9

2.97

2.03

4.89

4.16

3.88

3.02

Samanta

289

6.7

64.8

2.63

1.61

4.59

3.48

3.29

3.01

MCL

617

6.2

29.2

2.58

1.22

3.87

4.02

3.77

2.83

Chen

577

8.4

10.1

2.61

2.08

4.13

4.36

3.84

3.05

Rives

217

21.5

13.5

3.04

2.34

4.22

4.14

3.97

3.03

SPC

85

54.9

13.4

1.33

0.87

2.65

2.11

2.51

2.29

DIP Yeast PPI network

CASCADE

50

48.1

7.3

14.1

7.84

15.8

12.1

12.8

9.09

STM

60

40.1

7.8

13.0

7.23

14.2

11.8

11.9

8.04

Maximal clique

120

5.7

98.3

10.2

7.67

10.0

8.46

10.0

6.57

Quasi clique

103

11.2

80.8

11.0

6.29

12.0

10.7

11.1

7.69

Samanta

64

7.9

79.9

8.76

4.74

10.7

9.82

10.8

8.01

Minimum cut

114

13.5

35.0

7.97

4.58

8.56

8.19

7.87

6.21

Betweenness cut

180

10.3

21.0

7.89

4.06

8.59

7.02

6.98

4.88

MCL

163

9.8

36.7

8.08

3.84

9.53

7.81

8.11

6.26

Chen

141

16.3

1.7

9.12

4.91

9.87

8.28

8.09

6.01

Rives

42

55.3

7.8

10.1

6.88

9.52

9.61

9.59

7.42

SPC

5

47.2

6.4

5.27

2.39

5.49

6.23

5.91

5.18