A Least Square Method Based Model for Identifying Protein Complexes in Protein-Protein Interaction Network

Table 1

Comparison on biological relevance of complexes predicted by the algorithms.

Network	Method	MF	BP	CC
Krogan	PLSMC	0.479	0.457	0.592
	SLCP2	0.394	0.114	0.094
	ClusterONE	0.311	0.291	0.357
	RSGNM	0.392	0.270	0.270
	OCG	0.199	0.185	0.331
	MCL	0.265	0.057	0.033
	CFinder	0.296	0.287	0.330
Collins	PLSMC	0.536	0.460	0.620
	SLCP2	0.405	0.353	0.410
	ClusterONE	0.401	0.377	0.419
	RSGNM	0.376	0.371	0.418
	OCG	0.519	0.439	0.612
	MCL	0.380	0.240	0.331
	CFinder	0.439	0.351	0.439
Gavin	PLSMC	0.399	0.362	0.467
	SLCP2	0.374	0.153	0.189
	ClusterONE	0.374	0.308	0.360
	RSGNM	0.382	0.333	0.389
	OCG	0.381	0.310	0.405
	MCL	0.308	0.112	0.210
	CFinder	0.387	0.350	0.401
BioGRID	PLSMC	0.459	0.452	0.511
	SLCP2	0.443	0.184	0.117
	ClusterONE	0.439	0.447	0.439
	RSGNM	0.363	0.277	0.267
	OCG	0.262	0.321	0.343
	MCL	0.400	0.176	0.140
	CFinder	—	—	—
CYC2008		0.458	0.424	0.525

MF, molecular function; BP, biological process; CC, cellular compartment.