A density-based clustering approach for identifying overlapping protein complexes with functional preferences

Hu, Lun; Chan, Keith CC

doi:10.1186/s12859-015-0583-3

BMC Bioinformatics

Table 3 Results of f -measure, Accuracy and MMR

From: A density-based clustering approach for identifying overlapping protein complexes with functional preferences

PPI network	Approach	# ^{^}	Coverage ^*	f -measure			Accuracy	MMR
PPI network	Approach	# ^{^}	Coverage ^*	Precision	Recall	f -measure	Accuracy	MMR
Krogan	DCAFP	1195	1704	0.54	0.46	0.5^(1st)	0.51^(2nd)	0.23^(3rd)
	PCIA	1210	2630	0.34	0.66	0.45^(2nd)	0.5^(3rd)	0.33^(1st)
	GMFTP	297	1411	0.49	0.39	0.43	0.52^(1st)	0.18
	MCL	545	2674	0.33	0.46	0.38	0.45	0.2
	MCODE	71	617	0.7	0.16	0.26	0.39	0.06
	RNSC	752	2145	0.33	0.57	0.42	0.46	0.27^(2nd)
	IPCA	396	820	0.26	0.52	0.35	0.47	0.13
	CFinder	261	1140	0.73	0.31	0.44^(3rd)	0.49	0.16
	CMC	297	939	0.44	0.34	0.38	0.49	0.15
	COACH	347	1056	0.59	0.33	0.42	0.48	0.17
Gavin	DCAFP	955	1176	0.56	0.38	0.45^(1st)	0.46	0.19^(1st)
	PCIA	268	1415	0.5	0.35	0.41	0.47^(3rd)	0.14^(3rd)
	GMFTP	161	917	0.69	0.32	0.44^(2nd)	0.53^(1st)	0.13
	MCL	189	1430	0.51	0.29	0.37	0.46	0.11
	MCODE	69	645	0.68	0.15	0.25	0.38	0.06
	RNSC	309	1262	0.47	0.42	0.44^(2nd)	0.49^(2nd)	0.17^(2nd)
	IPCA	455	915	0.46	0.22	0.3	0.39	0.11
	CFinder	267	1124	0.71	0.3	0.42^(3rd)	0.45	0.14^(3rd)
	CMC	307	964	0.36	0.3	0.33	0.43	0.13
	COACH	322	1052	0.51	0.32	0.39	0.42	0.14^(3rd)
Collins	DCAFP	1083	1271	0.69	0.44	0.54^(2nd)	0.47	0.23^(3rd)
	PCIA	494	1607	0.55	0.56	0.55^(1st)	0.55^(3rd)	0.27^(1st)
	GMFTP	192	1160	0.67	0.37	0.48	0.57^(1st)	0.16
	MCL	297	1620	0.61	0.5	0.55^(1st)	0.56^(2nd)	0.23^(3rd)
	MCODE	111	857	0.82	0.28	0.42	0.53	0.12
	RNSC	356	1486	0.57	0.53	0.55^(1st)	0.57^(1st)	0.26^(2nd)
	IPCA	312	938	0.51	0.22	0.31	0.35	0.12
	CFinder	318	1160	0.59	0.34	0.43	0.41	0.19
	CMC	174	1075	0.65	0.34	0.45^(3rd)	0.52	0.15
	COACH	244	1114	0.57	0.34	0.43	0.4	0.16
DIP Scere	DCAFP	1643	2430	0.39	0.6	0.47^(2nd)	0.46^(2nd)	0.27^(3rd)
	PCIA	1823	4440	0.26	0.72	0.38	0.44	0.004
	GMFTP	473	2407	0.39	0.49	0.43	0.47^(1st)	0.2
	MCL	834	4579	0.23	0.45	0.3	0.36	0.19
	MCODE	62	795	0.44	0.09	0.15	0.27	0.03
	RNSC	1392	3791	0.22	0.67	0.33	0.39	0.28^(2nd)
	IPCA	3682	4579	0.19	0.65	0.29	0.43	0.39^(1st)
	CFinder	427	2143	0.58	0.43	0.49^(1st)	0.45^(3rd)	0.2
	CMC	1152	1775	0.29	0.56	0.38	0.45^(3rd)	0.28^(2nd)
	COACH	853	1952	0.39	0.52	0.45^(3rd)	0.4	0.24
DIP Hsapi	DCAFP	1091	2124	0.39	0.29	0.333^(1st)	0.32^(2nd)	0.08^(2nd)
	PCIA	855	2178	0.36	0.3	0.327^(2nd)	0.33^(1st)	0.001
	GMFTP	196	827	0.37	0.13	0.19	0.27	0.02
	MCL	556	2434	0.3	0.2	0.24	0.3	0.04
	MCODE	69	313	0.49	0.05	0.09	0.21	0.008
	RNSC	738	1846	0.33	0.25	0.28^(3rd)	0.29	0.06^(3rd)
	IPCA	1733	2434	0.19	0.23	0.21	0.33^(1st)	0.11^(1st)
	CFinder	134	515	0.64	0.13	0.22	0.31^(3rd)	0.02
	CMC	136	417	0.58	0.13	0.21	0.28	0.02
	COACH	150	491	0.67	0.14	0.23	0.32^(2nd)	0.02

^{^}The total number of identified protein complexes.
^*The total number of distinct proteins found in all identified complexes.

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