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Table 6 Main features of the four large scale data sets and clustering performances of the algorithms when applied to them

From: Evaluation of clustering algorithms for protein-protein interaction networks

Dataset

Nb nodes

Nb edges

Mean degree

Mean clust coeff

 

MCL

MCODE

RNSC

SPC

      

real

permuted

real

permuted

real

permuted

real

permuted

Uetz et al. [1]

926

865

1.175

0.018

Number of clusters

288

10

48

234

     

Mean nb prot/cluster

3.22

11.2

1.91

3.96

     

Median nb prot/cluster

3

4.5

2

2

     

Largest cluster size

16

53

6

276

     

Sn

57.3%

38.6%

84.3%

74.5%

49.4%

36.5%

65.5%

43.3%

     

PPV

53.8%

45.9%

25.5%

21.6%

59.6%

54.4%

38.0%

38.9%

     

Acc g

55.6%

42.3%

54.9%

48.0%

54.5%

45.5%

51.8%

41.1%

     

Sep co

23.0%

20.6%

48.9%

62.5%

15.5%

14.8%

19.1%

21.2%

     

Sep cl

30.1%

26.9%

2.2%

2.8%

34.3%

32.7%

20.3%

22.6%

     

Sep

26.3%

23.5%

10.4%

13.3%

23.1%

22.0%

19.7%

21.9%

Ito et al. [2]

2937

4038

2.682

0.019

Number of clusters

630

9

1746

410

     

Mean nb prot/cluster

4.66

97.8

1.68

7.16

     

Median nb prot/cluster

3

11

2

2

     

Largest cluster size

157

485

4

1928

     

Sn

34.9%

26.0%

66.9%

68.0%

31.4%

24.0%

73.2%

64.6%

     

PPV

42.7%

38.5%

8.2%

5.8%

63.6%

61.8%

24.3%

23.8%

     

Acc g

38.8%

32.2%

37.5%

36.9%

47.5%

42.9%

48.8%

44.2%

     

Sep co

12.7%

11.8%

41.6%

33.0%

7.1%

7.0%

11.3%

11.0%

     

Sep cl

36.2%

33.9%

1.7%

1.3%

56.7%

55.9%

20.1%

20.4%

     

Sep

21.4%

20%

8.4%

6.7%

20.1%

19.8%

15.4%

15.0%

Ho et al. [5]

1564

3600

4.6

0.029

Number of clusters

314

13

957

63

     

Mean nb prot/cluster

4.98

49.5

1.63

24.8

     

Median nb prot/cluster

3

13

1

3

     

Largest cluster size

34

432

8

1383

     

Sn

50.6%

28.2%

81.2%

76.5%

37.0%

27.4%

90.1%

92.1%

     

PPV

47.1%

35.6%

12.9%

8.5%

61.5%

57.1%

10.4%

8.2%

     

Acc g

48.9%

31.9%

47.1%

42.5%

49.3%

42.2%

50.2%

50.2%

     

Sep co

22.6%

19%

44.7%

37.2%

11%

10.5%

19.3%

13.8%

     

Sep cl

32.3%

27.1%

2.6%

2.2%

48%

45.6%

5.5%

4.0%

     

Sep

27.0%

22.7%

10.9%

9.0%

23%

21.9%

10.3%

7.4%

Gavin et al. [4]

1352

3210

4.7

0.148

Number of clusters

212

27

709

87

     

Mean nb prot/cluster

6.38

32.5

1.91

15.5

     

Median nb prot/cluster

4

7

1

2

     

Largest cluster size

54

414

16

1074

     

Sn

74.1%

24.2%

67.0%

51.1%

52.1%

20.8%

91.8%

81.4%

     

PPV

57.0%

23.9%

20.4%

9.4%

62.0%

46.0%

18.1%

10.7%

     

Acc g

65.6%

24.0%

43.7%

30.3%

57.1%

33.4%

54.9%

46.0%

     

Sep co

39.4%

17.6%

44.5%

16.1%

14.5%

11.3%

34.4%

15.7%

     

Sep cl

38.0%

17.0%

5.5%

2.0%

46.9%

36.5%

13.6%

6.2%

     

Sep

38.7%

17.3%

15.6%

5.6%

26.1%

20.3%

21.6%

9.8%

Gavin et al. [6]

1430

6531

9.1

0.348

Number of clusters

189

39

487

136

     

Mean nb prot/cluster

7.57

40.3

2.94

10.5

     

Median nb prot/cluster

4

9

2

3

     

Largest cluster size

90

697

35

620

     

Sn

75.7%

23.7%

58.3%

43.2%

60.8%

20.9%

79.8%

48.4%

     

PPV

54.3%

21.0%

20.6%

8.0%

63.3%

37.3%

37.0%

16.5%

     

Acc g

65.0%

22.4%

39.5%

25.6%

62.1%

29.1%

58.4%

32.4%

     

Sep co

38.1%

15.5%

44.7%

15.3%

20.1%

12.9%

34.9%

14.9%

     

Sep cl

32.7%

13.3%

7.9%

2.7%

44.5%

28.6%

21.6%

9.2%

     

Sep

35.3%

14.4%

18.8%

6.4%

29.9%

19.2%

27.4%

11.7%

Krogan et al. [7]

2675

7088

5.296

0.146

Number of clusters

813

70

1405

114

     

Mean nb prot/cluster

4.93

28.3

2.1

10.3

     

Median nb prot/cluster

3

5.5

2

3

     

Largest cluster size

50

387

21

1724

     

Sn

62.8%

19.8%

56.3%

30.9%

53.1%

19.1%

82.6%

64.0%

     

PPV

56.2%

33.5%

21.9%

9.7%

63.3%

51.1%

25.4%

17.2%

     

Acc g

59.5%

26.7%

39.1%

20.3%

58.2%

35.1%

54.0%

40.6%

     

Sep co

20.0%

12.1%

33.2%

13.6%

10.3%

8.7%

20.3%

11.9%

     

Sep cl

49.5%

29.9%

8.8%

3.6%

59.6%

50.3%

24.0%

14.1%

     

Sep

31.5%

19.0%

17.0%

7.0%

24.7%

21.6%

20.9%

12.9%