Evaluation and comparison of mammalian subcellular localization prediction methods

BMC Bioinformatics

Table 2 Evaluation of subcellular prediction methods on SP3763 (A) and LOC2145 (B)

A) SP3763	CELLO		MultiLoc		Proteome Analyst		pTarget		WoLFPSORT		Theoretical
	Sens	Spec	Sens	Spec	Sens	Spec	Sens	Spec	Sens	Spec	Sens	Spec
overall	0.58		0.51		0.77 (0.65)		0.49		0.61
nucleus	0.83	0.63	0.55	0.79	0.87 (0.80)	0.91	0.62	0.78	0.75	0.74	0.11	0.30
cytosol	0.27	0.40	0.51	0.39	0.57 (0.49)	0.56	0.41	0.40	0.40	0.41	0.11	0.17
mitochondrion	0.45	0.51	0.41	0.53	0.66 (0.55)	0.81	0.50	0.50	0.45	0.41	0.11	0.09
extracellular region	0.47	0.82	0.41	0.81	0.70 (0.58)	0.90	0.30	0.88	0.62	0.84	0.11	0.41
plasma membrane	0.38	0.28	0.38	0.26	0.10 (0.07)	0.38	0.42	0.33	0.45	0.36	0.11	0.11
Golgi apparatus	0.04	0.80	0.08	0.08	0.48 (0.41)	0.45	0.24	0.12	0.02	0.33	0.11	0.03
endoplasmic reticulum	0.03	0.22	0.16	0.08	0.57 (0.43)	0.19	0.32	0.11	0.05	0.05	0.11	0.02
peroxisome	0.30	0.67	0.55	0.07	0.46 (0.30)	0.55	0.55	0.08	0.05	0.03	0.11	0.01
lysosome	0.24	0.10	0.24	0.05	0.50 (0.43)	0.19	0.19	0.02	0	0	0.11	0.01
B) LOC2145
overall	0.44		0.43		0.56 (0.43)		0.45		0.43
nucleus	0.62	0.55	0.36	0.70	0.67 (0.57)	0.92	0.42	0.71	0.49	0.71	0.11	0.26
cytosol	0.23	0.08	0.39	0.08	0.63 (0.51)	0.18	0.34	0.10	0.32	0.07	0.11	0.04
mitochondrion	0.60	0.48	0.54	0.57	0.83 (0.77)	0.80	0.59	0.43	0.52	0.43	0.11	0.08
extracellular region	0.65	0.30	0.58	0.33	0.92 (0.90)	0.34	0.52	0.52	0.84	0.33	0.11	0.10
plasma membrane	0.44	0.57	0.53	0.76	0.16 (0.10)	0.76	0.51	0.74	0.54	0.65	0.11	0.33
Golgi apparatus	0.05	0.78	0.25	0.44	0.58 (0.50)	0.73	0.30	0.33	0.03	1.00	0.11	0.07
endoplasmic reticulum	0.03	0.83	0.14	0.27	0.61 (0.48)	0.56	0.31	0.35	0.07	0.22	0.11	0.08
peroxisome	0.12	1.00	0.46	0.17	0.31 (0.20)	0.92	0.51	0.24	0.04	0.06	0.11	0.03
lysosome	0.05	0.25	0.09	0.11	0.17 (0.13)	0.50	0.17	0.09	0	0.06	0.11	0.04

The individual sensitivity (Sens) and specificity (Spec) achieved by each predictor overall and individual locations was calculated. Values when all unpredicted subcellular locations are regarded as failed (i.e. false negative) are shown in parentheses. When calculating the overall sensitivity, a true positive was assigned for proteins with multiple subcellular locations when any of the locations were correctly predicted.

ISSN: 1471-2105