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.

Srihari et al. BMC Bioinformatics 2010 11:504   doi:10.1186/1471-2105-11-504

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