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Table 7 Existing complex detection methods selected for comparisons with MCL-CAw

From: MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure

  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]
  1. 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.