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

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

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%
  1. 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