Detecting overlapping protein complexes based on a generative model with functional and topological properties

BMC Bioinformatics

Table 3 Benchmark results using both the PPI network and the total GO annotation with respect to the CYC2008 gold standard

Network	Algorithm	GO sim	Coverage	# Complexes	FRAC	MMR	ACC	PR
Collins	GMFTP	–	1085	188	0.890	0.659	0.788	0.651
		Jiang	1210	169	0.868	0.575	0.784	0.579
	ClusterONE	Kappa	1130	161	0.840	0.573	0.770	0.597
		Lin	1255	172	0.854	0.561	0.784	0.613
Gavin	GMFTP	–	1122	208	0.877	0.594	0.768	0.577
		Jiang	1298	224	0.833	0.549	0.768	0.496
	ClusterONE	Kappa	1218	217	0.783	0.511	0.760	0.485
		Lin	1461	253	0.804	0.514	0.757	0.449
Krogan core	GMFTP	–	1218	252	0.805	0.573	0.768	0.649
		Jiang	1516	341	0.847	0.540	0.756	0.445
	ClusterONE	Kappa	1322	319	0.810	0.522	0.736	0.470
		Lin	1813	464	0.841	0.517	0.766	0.379
Krogan extended	GMFTP	–	1062	216	0.696	0.487	0.745	0.601
		Jiang	2021	503	0.724	0.435	0.745	0.342
	ClusterONE	Kappa	1722	482	0.680	0.410	0.733	0.344
		Lin	2458	752	0.713	0.425	0.730	0.281
DIP	GMFTP	–	1492	306	0.705	0.430	0.704	0.474
		Jiang	2910	733	0.741	0.406	0.714	0.299
	ClusterONE	Kappa	2487	748	0.679	0.398	0.682	0.308
		Lin	3285	921	0.701	0.359	0.700	0.248
BioGRID	GMFTP	–	2283	413	0.750	0.474	0.754	0.448
		Jiang	3789	881	0.665	0.377	0.759	0.260
	ClusterONE	Kappa	3303	889	0.691	0.398	0.717	0.283
		Lin	4208	1073	0.602	0.334	0.755	0.227

ISSN: 1471-2105