Genome-wide subcellular localization of putative outer membrane and extracellular proteins in Leptospira interrogans serovar Lai genome using bioinformatics approaches

Table 1 Localization predictions of a set of 299 experimentally verified proteins with known localization

Actual localization	Total	TP	FP	FN	TN	Precision	Recall
PSORTb
CP	145	110	1	35	110	99.10%	75.86%
CM	69	55	2	14	166	96.49%	79.71%
PP	29	18	0	11	207	100.00%	62.07%
OM	38	30	0	8	195	100.00%	78.95%
EX	18	6	3	12	216	66.67%	33.33%
Total	299	219	6	80	894	97.33%	73.24%
Proteome Analyst
CP	145	94	0	51	119	100.00%	64.83%
CM	69	59	2	10	162	96.72%	85.51%
PP	29	19	3	10	201	86.36%	65.52%
OM	38	31	0	7	192	100.00%	81.58%
EX	18	9	6	9	207	60.00%	50.00%
Total	299	212	11	87	881	95.07%	70.90%
ProtCompB
CP	145	127	11	18	144	92.03%	87.59%
CM	69	55	7	14	227	88.71%	79.71%
PP	29	19	9	10	261	67.86%	65.52%
OM	38	23	18	15	243	56.10%	60.53%
EX	18	11	4	7	277	73.33%	61.11%
Total	299	235	49	64	1152	82.75%	78.60%
Consensus vote
CP	145	67	0	78	154	100.00%	46.21%
CM	69	43	0	26	230	100.00%	62.32%
PP	29	11	0	18	270	100.00%	37.93%
OM	38	19	0	19	261	100.00%	50.00%
EX	18	4	0	13	216	100.00%	23.53%
Total	299	144	0	154	1131	100.00%	48.32%
Majority vote (2 out of 3 predictions)
CP	145	121	0	24	154	100.00%	83.45%
CM	69	59	0	10	230	100.00%	85.51%
PP	29	17	0	12	270	100.00%	58.62%
OM	38	29	0	10	213	100.00%	74.36%
EX	18	6	1	12	215	85.71%	33.33%
Total	299	232	1	68	1082	99.57%	77.33%
Combination method
CP	N/A	N/A	N/A	N/A	N/A	N/A	N/A
CM	N/A	N/A	N/A	N/A	N/A	N/A	N/A
PP	29	25	0	4	56	100.00%	86.20%
OM	38	34	1	4	46	97.14%	89.47%
EX	18	12	2	6	65	85.71%	66.67%
Total	85	71	3	14	167	95.95%	87.53%

299 proteins obtained from the test set used in comparison study by Gardy and Brinkman [22] Majority vote is the result from 2 out of 3 predictions. Combination method: the result from non-consensus vote with significant DBsubloc [31] and/or GTD prediction [32] Precision is calculated as TP/(TP+FP), Recall is calculated as TP/(TP+FN) TP = true positive, TN = true negative, FP = false positive, FN = false negative, N/A= Not applicable

ISSN: 1471-2164