Skip to main content

Table 1 Comparison of predicted and experimental gene essentiality using different networks and different growth conditions.

From: Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

Network Experiment
Condition
Threshold Number of Gene Essentiality Predictions Sensitivity Specificity Matthews Correlation Coefficient
    TP FN FP TN    
iNJ 661 In vitro <1.0 153 84 71 236 0.65 0.77 0.42
iNJ 661m In vitro <1.0 153 85 71 237 0.64 0.77 0.42
GSMN-TB In vitro <1.0 156 85 58 294 0.65 0.84 0.49
GSMN-TBv In vitro <1.0 160 81 75 277 0.66 0.79 0.45
iNJ 661v In vitro <1.0 140 98 80 228 0.59 0.74 0.33
iNJ 661 In vitro ≤0.2 135 102 59 248 0.57 0.81 0.39
iNJ 661m In vitro ≤0.2 135 103 59 249 0.57 0.81 0.39
GSMN-TB In vitro ≤0.2 152 89 47 305 0.63 0.87 0.52
GSMN-TBv In vitro ≤0.2 156 85 65 287 0.65 0.82 0.47
iNJ 661v In vitro ≤0.2 123 115 63 245 0.52 0.80 0.33
iNJ 661 In vivo <1.0 16 20 97 242 0.44 0.71 0.10
iNJ 661m In vivo <1.0 16 20 94 246 0.44 0.72 0.11
GSMN-TB In vivo <1.0 10 34 76 317 0.23 0.81 0.03
GSMN-TBv In vivo <1.0 16 28 93 300 0.36 0.76 0.09
iNJ 661v In vivo <1.0 31 5 77 263 0.86 0.77 0.41
iNJ 661 In vivo ≤0.2 11 25 76 263 0.31 0.78 0.06
iNJ 661m In vivo ≤0.2 11 25 76 264 0.31 0.78 0.06
GSMN-TB In vivo ≤0.2 10 34 65 328 0.23 0.83 0.05
GSMN-TBv In vivo ≤0.2 16 28 83 310 0.36 0.79 0.11
iNJ 661v In vivo ≤0.2 29 7 52 288 0.81 0.85 0.47
  1. A true positive (TP) prediction refers to a gene correctly predicted to be essential, whereas a false negative (FN) prediction refers to a gene incorrectly predicted to be non-essential. A false positive (FP) prediction refers to a gene incorrectly predicted to be essential, whereas a true negative (TN) prediction refers to a gene correctly predicted to be non-essential. Sensitivity = TP/(TP + FN). Specificity = TN/(TN + FP). Matthews correlation coefficient = (TP × TN - FP × FN)/[(TP + FP)(TP + FN)(TN + FP)(TN + FN)]1/2. GSMN-TBv indicates the GSMN-TB network with its in vivo biomass objective function.