Protein-protein interaction as a predictor of subcellular location

BMC Systems Biology

Table 2 Evaluation of prediction method variants on human reference and supported subsets

PPI sets	DISCRETE				MERGED				COMMON				MAJORITY
	PA	SA	PA (M)	SA (M)	PA	SA	PA (M)	SA (M)	PA	SA	PA (M)	SA (M)	PA	SA	PA (M)	SA (M)
Reference	0.64	0.35	0.50	0.27	0.72	0.26	0.62	0.23	0.65	0.40	0.53	0.32	0.68	0.34	0.58	0.27
BPscore	0.84	0.56	0.76	0.46	0.86	0.55	0.79	0.42	0.85	0.57	0.77	0.47	0.86	0.55	0.79	0.43
Interologs	0.85	0.58	0.70	0.46	0.84	0.54	0.69	0.42	0.83	0.57	0.67	0.45	0.84	0.56	0.69	0.45
DDI	0.72	0.46	0.65	0.43	0.75	0.43	0.70	0.42	0.72	0.48	0.66	0.49	0.74	0.45	0.69	0.44
PMID	0.76	0.46	0.60	0.28	0.76	0.42	0.60	0.27	0.74	0.45	0.56	0.30	0.76	0.43	0.59	0.28
Method	0.74	0.38	0.61	0.29	0.76	0.37	0.63	0.27	0.73	0.41	0.58	0.32	0.75	0.38	0.62	0.29
DB	0.73	0.37	0.53	0.25	0.74	0.35	0.61	0.26	0.71	0.40	0.57	0.30	0.73	0.37	0.59	0.28
ALL	0.74	0.42	0.61	0.35	0.78	0.38	0.69	0.33	0.74	0.45	0.64	0.40	0.76	0.41	0.67	0.36
BIO	0.77	0.49	0.67	0.43	0.79	0.45	0.71	0.38	0.77	0.50	0.67	0.45	0.78	0.47	0.70	0.41
EVI	0.74	0.37	0.55	0.25	0.75	0.34	0.62	0.25	0.71	0.41	0.57	0.30	0.74	0.37	0.61	0.27

ALL: Union of all subsets (BPscore ∪ Interologs ∪ DDI ∪ PMID ∪ Method ∪ DB)
BIO: Union of biological evidence type subsets (BPscore ∪ Interologs ∪ DDI)
EVI: Union of recorded evidence type subsets (PMID ∪ Method ∪ DB)
M: Interactions involving an integral membrane protein
The permissive accuracy (PA) and strict accuracy (SA) were calculated for all variants (DISCRETE, MERGED, COMMON and MAJORITY) for all interactions, and for interactions involving an integral membrane protein (M).

ISSN: 1752-0509