Table 2 Statistics of predicted complexes by five algorithms with the best parameters optimized on CYC08 and YHTP08 sets and the DIP PPI network as input.
From: Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity
Algorithm | Gold Standard Sets | |
|---|---|---|
(optimized parameters) | CYC08 (236/6.7) | YHTP08 (207/8.2) |
COACH | 271/113/7.3 | 271/95/7.3 |
(affinity threshold) | (0.1) | (0.1) |
MCODE | 57/25/12.9 | 57/18/12.9 |
(VWP) | (0.2) | (0.2) |
MCL | 830/123/5.9 | 830/115/5.9 |
(inflation) | (1.75) | (1.75) |
DME | 487/44/25.1 | 503/40/24.7 |
(density threshold) | (0.97) | (0.96) |
miPALM | 238/100/7.0 | 277/88/7.0 |
(α, δ) | (0.364, 2.40) | (0.374, 2.33) |