Skip to main content

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