Table 7 Functional enrichment analysis of protein complexes detected by different methods in Collins, Gavin and Krogan datasets
From: Detecting protein complexes with multiple properties by an adaptive harmony search algorithm
Method | \({\mathbf{ < }}\left( {\varvec{E}{\mathbf{ - 20}}} \right)\) | [E-20,E-15) | [E-15,E-10) | [E-10,E-5) | [E-5,0.01) | \(\leqslant {\mathbf{0.01}}\) |
|---|---|---|---|---|---|---|
Collins dataset | ||||||
MCL | 62(39.24%) | 9(5.7%) | 25(15.82%) | 40(25.32%) | 4(2.53%) | 140(88.61%) |
IPCA | 108(31.58%) | 37(10.82%) | 63(18.42%) | 97(28.36%) | 16(4.68%) | 321(93.86%) |
COACH | 64(25.5%) | 22(8.76%) | 39(15.54%) | 80(31.87%) | 14(5.58%) | 219(87.25%) |
CMC | 54(30.51%) | 17(9.6%) | 22(12.43%) | 63(35.59%) | 8(4.52%) | 164(92.66%) |
SPICi | 62(51.24%) | 10(8.26%) | 19(15.7%) | 25(20.66%) | 3(2.48%) | 119(98.35%)\(^{1st}\) |
ClusterONE | 47(23.15%) | 19(9.36%) | 45(22.17%) | 61(30.05%) | 11(5.42%) | 183(90.15%) |
PEWCC | 128(30.05%) | 21(4.93%) | 104(24.41%) | 120(28.17%) | 18(4.23%) | 391(91.78%) |
WPNCA | 90(33.46%) | 33(12.27%) | 61(22.68%) | 52(19.33%) | 7(2.6%) | 243(90.33%) |
WEC | 394(40.74%) | 81(8.38%) | 174(17.99%) | 261(26.99%) | 23(2.38%) | 933(96.48%) |
ClusterEPs | 4(0.68%) | 13(2.21%) | 95(16.18%) | 350(59.63%) | 74(12.61%) | 536(91.31%) |
ClusterSS | 22(10.05%) | 19(8.68%) | 48(21.92%) | 93(42.47%) | 18(8.22%) | 200(91.32%) |
28(12.96%) | 25(11.57%) | 45(20.83%) | 85(39.35%) | 19(8.8%) | 202(93.52%) | |
SE-DMTG | 58(34.73%) | 22(13.17%) | 29(17.37%) | 46(27.54%) | 6(3.59%) | 161(96.41%) |
MPC-C | 75(27.37%) | 35(12.77%) | 49(17.88%) | 86(31.39%) | 10(3.65%) | 255(93.07%) |
GCC-v | 11(5.16%) | 19(8.92%) | 28(13.15%) | 107(50.23%) | 29(13.62%) | 194(91.08%) |
MP-AHSA | 75(27.17%) | 36(13.04%) | 48(17.39%) | 94(34.06%) | 15(5.43%) | 268(97.1%)\(^{2nd}\) |
Gavin dataset | ||||||
MCL | 24(10.91%) | 22(10.0%) | 35(15.91%) | 72(32.73%) | 22(10.0%) | 175(79.55%) |
IPCA | 121(26.08%) | 58(12.5%) | 70(15.09%) | 106(22.84%) | 41(8.84%) | 396(85.34%) |
COACH | 124(34.35%) | 34(9.42%) | 52(14.4%) | 83(22.99%) | 18(4.99%) | 311(86.15%) |
CMC | 71(24.15%) | 15(5.1%) | 40(13.61%) | 76(25.85%) | 21(7.14%) | 223(75.85%) |
SPICi | 47(24.87%) | 15(7.94%) | 30(15.87%) | 54(28.57%) | 17(8.99%) | 163(86.24%) |
ClusterONE | 52(20.16%) | 11(4.26%) | 36(13.95%) | 78(30.23%) | 20(7.75%) | 197(76.36%) |
PEWCC | 76(11.45%) | 51(7.68%) | 108(16.27%) | 224(33.73%) | 77(11.6%) | 536(80.72%) |
WPNCA | 128(26.45%) | 32(6.61%) | 100(20.66%) | 158(32.64%) | 19(3.93%) | 437(90.29%) |
WEC | 261(28.87%) | 82(9.07%) | 151(16.7%) | 234(25.88%) | 66(7.3%) | 794(87.83%) |
ClusterEPs | 74(27.31%) | 35(12.92%) | 47(17.34%) | 62(22.88%) | 22(8.12%) | 240(88.56%) |
ClusterSS | 27(6.47%) | 24(5.76%) | 57(13.67%) | 178(42.69%) | 50(11.99%) | 336(80.58%) |
30(7.59%) | 21(5.32%) | 68(17.22%) | 165(41.77%) | 42(10.63%) | 326(82.53%) | |
SE-DMTG | 82(35.65%) | 35(15.22%) | 38(16.52%) | 48(20.87%) | 13(5.65%) | 216(93.91%)\(^{2nd}\) |
MPC-C | 124(31.16%) | 38(9.55%) | 58(14.57%) | 152(38.19%) | 10(2.51%) | 382(95.98%)\(^{1st}\) |
GCC-v | 13(4.45%) | 15(5.14%) | 27(9.25%) | 101(34.59%) | 44(15.07%) | 200(68.49%) |
MP-AHSA | 100(27.17%) | 30(8.15%) | 58(15.76%) | 125(33.97%) | 32(8.7%) | 345(93.75%) |
Krogan dataset | ||||||
MCL | 31(8.38%) | 23(6.22%) | 40(10.81%) | 118(31.89%) | 31(8.38%) | 243(65.68%) |
IPCA | 101(17.35%) | 70(12.03%) | 90(15.46%) | 218(37.46%) | 39(6.7%) | 518(89.0%) |
COACH | 68(19.71%) | 33(9.57%) | 53(15.36%) | 118(34.2%) | 27(7.83%) | 299(86.67%) |
CMC | 36(13.64%) | 19(7.2%) | 38(14.39%) | 92(34.85%) | 21(7.95%) | 206(78.03%) |
SPICi | 10(4.46%) | 17(7.59%) | 42(18.75%) | 68(30.36%) | 25(11.16%) | 162(72.32%) |
ClusterONE | 34(14.17%) | 16(6.67%) | 34(14.17%) | 109(45.42%) | 14(5.83%) | 207(86.25%) |
PEWCC | 146(37.53%) | 50(12.85%) | 71(18.25%) | 95(24.42%) | 16(4.11%) | 378(97.17%)\(^{1st}\) |
WPNCA | 106(28.73%) | 52(14.09%) | 61(16.53%) | 114(30.89%) | 17(4.61%) | 350(94.85%) |
WEC | 171(33.14%) | 64(12.4%) | 88(17.05%) | 141(27.33%) | 19(3.68%) | 483(93.6%) |
ClusterEPs | 53(12.93%) | 32(7.8%) | 57(13.9%) | 237(57.8%) | 14(3.41%) | 393(95.85%) |
ClusterSS | 35(7.73%) | 33(7.28%) | 50(11.04%) | 188(41.5%) | 34(7.51%) | 340(75.06%) |
42(17.43%) | 33(13.69%) | 43(17.84%) | 92(38.17%) | 12(4.98%) | 222(92.12%) | |
SE-DMTG | 33(9.14%) | 33(9.14%) | 69(19.11%) | 173(47.92%) | 23(6.37%) | 331(91.69%) |
MPC-C | 93(20.39%) | 70(15.35%) | 110(24.12%) | 160(35.09%) | 7(1.54%) | 440(96.49%)\(^{2nd}\) |
GCC-v | 11(3.53%) | 9(2.88%) | 28(8.97%) | 148(47.44%) | 29(9.29%) | 225(72.12%) |
MP-AHSA | 75(14.71%) | 35(6.86%) | 90(17.65%) | 232(45.49%) | 27(5.29%) | 459(90.0%) |