Integrating domain similarity to improve protein complexes identification in TAP-MS data

Table 6 Evaluation results on Gavin_2006 network using CYC2008 gold-standard.

Quality measures	BGCA+BP	MCL	MCODE	CFinder	RRW	COACH	CODEC-w0	CODEC-w1
Sensitivity	0.480	0.538	0.338	0.390	0.089	0.596	0.584	0.582
PPV	0.709	0.571	0.342	0.365	0.764	0.120	0.511	0.546
Geometric accuracy	0.583	0.555	0.340	0.377	0.261	0.268	0.546	0.564
Complex-wise Homogeneity	0.326	0.295	0.123	0.087	0.088	0.048	0.234	0.272
Cluster-wise Homogeneity	0.896	0.816	0.748	0.613	0.989	0.030	0.086	0.107
Geometric Homogeneity	0.540	0.490	0.303	0.231	0.295	0.038	0.141	0.171
Precision	0.714	0.419	0.268	0.324	0.891	0.066	0.311	0.426
Recall	0.480	0.538	0.338	0.390	0.089	0.596	0.584	0.582
PR value	0.585	0.475	0.301	0.356	0.281	0.198	0.426	0.498
Cluster-wise Jaccard	0.583	0.335	0.208	0.260	0.633	0.053	0.169	0.230
Complex-wise Jaccard	0.380	0.319	0.146	0.139	0.082	0.272	0.362	0.383
Jaccard FMeasure	0.460	0.326	0.172	0.181	0.145	0.088	0.230	0.287
BH-Specificity	0.901	0.815	0.610	0.804	0.875	0.252	0.305	0.459
BH-Sensitivity	0.352	0.315	0.103	0.115	0.079	0.360	0.578	0.691
BH-FMeasure	0.506	0.454	0.176	0.201	0.144	0.297	0.399	0.552

ISSN: 1477-5956