Protein-protein interaction as a predictor of subcellular location

BMC Systems Biology

Table 3 Evaluation of SCL prediction methods using human union set (ALL)

PPI sets	COMMON	MAJORITY	MERGED	Proteome Analyst	WolfP SORT	CELLO	pTARGET
Membrane-membrane PPI only (162)
Total # of predicted proteins	155	162	162	35	162	162	79
# of correctly predicted proteins in PA	133	140	141	21	88	99	53
# of correctly predicted proteins in SA	92	91	84	9	61	56	38
PA	0.86	0.86	0.87	0.60	0.54	0.61	0.67
SA	0.59	0.56	0.52	0.26	0.38	0.35	0.48
Soluble-soluble PPI only (807)
Total # of predicted proteins	686	803	807	411	807	807	499
# of correctly predicted proteins in PA	556	669	689	343	508	605	308
# of correctly predicted proteins in SA	350	372	314	211	320	367	193
PA	0.81	0.83	0.85	0.83	0.63	0.75	0.62
SA	0.51	0.46	0.39	0.51	0.40	0.45	0.39
Membrane-soluble PPI only (206)
Total # of predicted proteins	193	205	206	64	206	206	95
# of correctly predicted proteins in PA	75	87	92	47	121	116	56
# of correctly predicted proteins in SA	39	37	35	32	92	75	39
PA	0.39	0.42	0.45	0.73	0.59	0.56	0.59
SA	0.20	0.18	0.17	0.50	0.45	0.36	0.41
Total (1175)
Total # of predicted proteins	1034	1170	1175	510	1175	1175	673
# of correctly predicted proteins in PA	764	896	922	411	717	820	417
# of correctly predicted proteins in SA	481	500	433	252	473	498	270
PA	0.74	0.77	0.78	0.81	0.61	0.70	0.62
SA	0.47	0.43	0.37	0.49	0.40	0.42	0.40

* Numbers in the parentheses indicate total number of proteins for prediction for each category

ISSN: 1752-0509