Table 3.
Benchmark results using both the PPI network and the total GO annotation with respect to the CYC2008 gold standard
| Network | Algorithm | GO sim | Coverage | # Complexes | FRAC | MMR | ACC | PR |
|---|---|---|---|---|---|---|---|---|
| Collins |
GMFTP |
– |
1085 |
188 |
0.890 |
0.659 |
0.788 |
0.651 |
| |
|
Jiang |
1210 |
169 |
0.868 |
0.575 |
0.784 |
0.579 |
| |
ClusterONE |
Kappa |
1130 |
161 |
0.840 |
0.573 |
0.770 |
0.597 |
| |
|
Lin |
1255 |
172 |
0.854 |
0.561 |
0.784 |
0.613 |
| Gavin |
GMFTP |
– |
1122 |
208 |
0.877 |
0.594 |
0.768 |
0.577 |
| |
|
Jiang |
1298 |
224 |
0.833 |
0.549 |
0.768 |
0.496 |
| |
ClusterONE |
Kappa |
1218 |
217 |
0.783 |
0.511 |
0.760 |
0.485 |
| |
|
Lin |
1461 |
253 |
0.804 |
0.514 |
0.757 |
0.449 |
| Krogan core |
GMFTP |
– |
1218 |
252 |
0.805 |
0.573 |
0.768 |
0.649 |
| |
|
Jiang |
1516 |
341 |
0.847 |
0.540 |
0.756 |
0.445 |
| |
ClusterONE |
Kappa |
1322 |
319 |
0.810 |
0.522 |
0.736 |
0.470 |
| |
|
Lin |
1813 |
464 |
0.841 |
0.517 |
0.766 |
0.379 |
| Krogan extended |
GMFTP |
– |
1062 |
216 |
0.696 |
0.487 |
0.745 |
0.601 |
| |
|
Jiang |
2021 |
503 |
0.724 |
0.435 |
0.745 |
0.342 |
| |
ClusterONE |
Kappa |
1722 |
482 |
0.680 |
0.410 |
0.733 |
0.344 |
| |
|
Lin |
2458 |
752 |
0.713 |
0.425 |
0.730 |
0.281 |
| DIP |
GMFTP |
– |
1492 |
306 |
0.705 |
0.430 |
0.704 |
0.474 |
| |
|
Jiang |
2910 |
733 |
0.741 |
0.406 |
0.714 |
0.299 |
| |
ClusterONE |
Kappa |
2487 |
748 |
0.679 |
0.398 |
0.682 |
0.308 |
| |
|
Lin |
3285 |
921 |
0.701 |
0.359 |
0.700 |
0.248 |
| BioGRID |
GMFTP |
– |
2283 |
413 |
0.750 |
0.474 |
0.754 |
0.448 |
| |
|
Jiang |
3789 |
881 |
0.665 |
0.377 |
0.759 |
0.260 |
| |
ClusterONE |
Kappa |
3303 |
889 |
0.691 |
0.398 |
0.717 |
0.283 |
| Lin | 4208 | 1073 | 0.602 | 0.334 | 0.755 | 0.227 |