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Table 4 Comparison of the functional enrichment of protein complexes with other algorithms on four datasets

From: iOPTICS-GSO for identifying protein complexes from dynamic PPI networks

Dataset

Algorithm

<E-15

[E-15, E-10]

[E-10, E-5]

[E-5, 0.01]

<0.01 significant

≥0.01 insignificant

DIP

COACH

33(6.96%)

44(9.28%)

205(43.25%)

126(26.58%)

408(86.08%)

66(13.92%)

MCL

19(1.80%)

47(4.46%)

183(17.38%)

362(34.38%)

611(58.02%)

442(41.98%)

MCODE

12(7.27%)

17(10.30%)

80(48.48%)

38(23.03%)

147(89.09%)

18(10.91%)

ClusterOne

21(3.66%)

52(9.06%)

177(30.84%)

184(32.06%)

434(75.61%)

140(24.39%)

OPTICS

7(7.87%)

13(14.61%)

40(44.94%)

21(23.6%)

81(91.01%)

8(8.99%)

OPTICS_PSO

5(6.85%)

10(13.70%)

27(36.99%)

23(31.51%)

65(89.04%)

8(10.96%)

iOPTICS-GSO

6(8.70%)

15(21.74%)

29(42.03%)

13(18.84%)

63(91.30%)

6(8.70%)

Krogan

COACH

23(10.41%)

37(16.74%)

91(41.18%)

54(24.43%)

205(92.76%)

16(7.24%)

MCL

16(3.97%)

43(10.67%)

103(25.56%)

119(29.53%)

281(69.73%)

122(30.27%)

MCODE

8(5.00%)

28(17.50%)

68(42.50%)

46(28.75%)

150(93.75%)

10(6.25%)

ClusterOne

13(3.26%)

43(10.78%)

98(24.56%)

120(30.08%)

274(68.67%)

125(31.33%)

OPTICS

13(8.44%)

26(16.88%)

56(36.36%)

31(20.13%)

126(81.82%)

28(18.18%)

OPTICS_PSO

9(9.47%)

19(20.0%)

41(43.16%)

21(22.11%)

90(94.74%)

5(5.26%)

iOPTICS-GSO

11(12.22%)

23(25.56%)

37(41.11%)

19(21.11%)

90(100%)

0(0%)

MIPS

COACH

16(4.04%)

46(11.62%)

145(36.62%)

149(37.63%)

356(89.9%)

40(10.10%)

MCL

5(0.83%)

13(2.15%)

94(15.51%)

220(36.30%)

332(54.79%)

274(45.21%)

MCODE

5(3.70%)

10(7.41%)

70(51.58%)

39(28.89%)

124(91.85%)

11(8.15%)

ClusterOne

7(1.88%)

16(4.30%)

117(31.45%)

126(33.87%)

266(71.51%)

106(28.49%)

OPTICS

16(5.63%)

6(2.11%)

26(9.15%)

74(26.06%)

122(42.96%)

162(57.04%)

OPTICS_PSO

10(11.76%)

3(3.53%)

28(32.94%)

30(35.29%)

71(83.53%)

14(16.47%)

iOPTICS-GSO

7(11.67%)

5(8.33%)

12(20%)

25(41.67%)

49(81.67%)

11(18.33%)

Gavin

COACH

35(14.96%)

39(16.67%)

100(42.72%)

55(23.50%)

229(97.86%)

5(2.14%)

MCL

22(9.69%)

34(14.98%)

88(38.77%)

66(29.07%)

110(92.51%)

17(7.49%)

MCODE

12(7.74%)

20(12.90%)

80(51.61%)

39(25.16%)

151(97.42%)

4(2.58%)

ClusterOne

31(10.62%)

34(11.64%)

118(40.41%)

82(28.08%)

292(90.75%)

27(9.25%)

OPTICS

20(18.52%)

13(12.04%)

53(49.07%)

19(17.59%)

105(97.22%)

3(2.78%)

OPTICS_PSO

15(18.07%)

13(15.66%)

38(45.78%)

16(19.28%)

82(98.80%)

1(1.20%)

iOPTICS-GSO

21(26.25%)

11(13.75%)

31(38.75%)

16(20%)

79(98.75%)

1(1.25%)

  1. The bold data in Tables 4 are the result of our four datasets