Skip to main content

Table 3 Result of comparison test

From: Improved method for protein complex detection using bottleneck proteins

PPI network dataset Reference dataset Algorithm Optimal parameters Number of protein complexes Recall Precision F1 score
DIP MIPS Proposed CC = 0.9, BC = 1% 269 0.5556 0.3086 0.3968
   [16] CC = 0.51, BC = 20% 76 0.3210 0.4605 0.3783
   Link Cluster Partition_density = 0.30 1,177 0.7037 0.1427 0.2373
   MCL Granularity = 2.00 614 0.5679 0.0739 0.1298
   MCODE Node_score = 0.10 83 0.2930 0.2530 0.2729
  CYC Proposed CC = 0.6, BC = 1% 646 0.4877 0.4860 0.4869
   [16] CC = 0.38, BC = 20% 333 0.3898 0.4114 0.4003
   Link Cluster Partition_density = 0.29 1,179 0.5932 0.2858 0.3857
   MCL Granularity = 2.40 639 0.4746 0.1690 0.2493
   MCODE Node_score = 0.10 83 0.2119 0.5542 0.3065
Bio-GRID MIPS Proposed. CC = 1.0, BC = 1% 127 0.3457 0.4724 0.3709
   [16] CC = 0.54, BC = 20% 69 0.2346 0.3623 0.2848
   Link Cluster Partition_density = 0.30 10,463 0.5926 0.0893 0.1552
   MCL Granularity = 3.60 216 0.2099 0.0556 0.0879
   MCODE Node_score = 0.10 120 0.086 0.0500 0.0633
  CYC Proposed CC = 1.0, BC = 15% 506 0.3260 0.3814 0.3515
   [16] CC = 0.43, BC = 30% 324 0.2500 0.2160 0.2318
   Link Cluster Partition_density = 0.28 10,915 0.5297 0.2802 0.3697
   MCL Granularity = 3.00 225 0.1144 0.1111 0.1127
   MCODE Node_score = 0.10 120 0.0593 0.1167 0.0787
I2D CORUM Proposed CC = 0.8, BC = 5% 2,508 0.4100 0.3545 0.3802
   [16] CC = 0.41, BC = 20% 1,132 0.2961 0.2491 0.2706
   Link Cluster Partition_density = 0.21 8,033 0.4576 0.1595 0.2378
   MCL Granularity = 1.60 750 0.0623 0.0587 0.0604
   MCODE Node_score = 0.10 251 0.0469 0.1076 0.0652
\