Table 7.
Existing complex detection methods selected for comparisons with MCL-CAw
| Method | |||||||
|---|---|---|---|---|---|---|---|
| Property | MCL | MCL-CA | MCLO | CORE | COACH | CMC | HACO |
| Principle | Flow simulation | Core-attach refinement over MCL | MCL with cluster overlaps | Core-attach by p-values | Core-attach by dense neighborhood | Maximal clique merging |
Hier agglo cluster with overlaps |
| Scored Networks | Yes | No | Yes | No | No | Yes | Yes |
| Unassigned Proteins | No | Yes | No | Yes | Yes | Yes | Yes |
|
Parameters (default) |
Inflation I (I = 2.5) |
Inflation I (I = 2.5) |
Inflation I , Overlap a, b (2.5, 1.0, 0.5) | / | Filter t (t = 0.225) |
Merge m, Overlap t, Min clust size (0.5, 0.25, 4) | UPGMA cutoff (0.2) |
| References | Dongen 2000 [18] |
Srihari et al. 2009 [28] |
Pu et al. 2007 [20] |
Leung et al. 2009 [24] |
Wu Min et al. 2009 [25] |
Liu et al. 2009 [16] |
Wang et al. 2009 [21] |
CORE (2009), COACH (2009), MCL-CA (2009) were compared against MCL-CAw only on the unscored Gavin+Krogan network, while MCL (2000, 2002), MCLO (2007), CMC (2009) and HACO (2009) were evaluated also on the scored networks.