Table 2 |
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|
Results with a naïve Bayes classifier. |
||||||||
|
Cross-validation |
Trained on: |
All |
All |
NoS |
All |
NoE |
All |
key |
|
Tested on: |
All |
NoS |
NoS |
NoE |
NoE |
key |
key |
|
|
|
||||||||
|
mixed |
AUC |
0.83 ± 0.01 |
0.70 ± 0.02 |
0.70 ± 0.02 |
0.81 ± 0.02 |
0.81 ± 0.02 |
0.80 ± 0.02 |
0.79 ± 0.01 |
|
MCC |
0.44 ± 0.04 |
0.27 ± 0.03 |
0.27 ± 0.03 |
0.43 ± 0.03 |
0.43 ± 0.03 |
0.41 ± 0.02 |
0.35 ± 0.06 |
|
|
Overall error rate |
0.19 ± 0.01 |
0.24 ± 0.01 |
0.24 ± 0.01 |
0.18 ± 0.01 |
0.18 ± 0.01 |
0.18 ± 0.01 |
0.21 ± 0.00 |
|
|
Effect error rate |
0.35 ± 0.05 |
0.52 ± 0.03 |
0.52 ± 0.03 |
0.26 ± 0.07 |
0.26 ± 0.07 |
0.24 ± 0.07 |
0.41 ± 0.04 |
|
|
No effect error rate |
0.15 ± 0.02 |
0.18 ± 0.01 |
0.18 ± 0.01 |
0.17 ± 0.01 |
0.17 ± 0.01 |
0.17 ± 0.02 |
0.17 ± 0.03 |
|
|
sensitivity |
0.47 ± 0.12 |
0.37 ± 0.06 |
0.37 ± 0.06 |
0.37 ± 0.06 |
0.37 ± 0.06 |
0.36 ± 0.09 |
0.38 ± 0.16 |
|
|
specificity |
0.92 ± 0.03 |
0.88 ± 0.02 |
0.88 ± 0.02 |
0.96 ± 0.02 |
0.96 ± 0.02 |
0.96 ± 0.03 |
0.92 ± 0.05 |
|
|
|
||||||||
|
lac rep |
AUC |
0.84 ± 0.02 |
0.74 ± 0.02 |
0.74 ± 0.02 |
0.82 ± 0.02 |
0.82 ± 0.02 |
0.80 ± 0.02 |
0.80 ± 0.02 |
|
MCC |
0.47 ± 0.03 |
0.33 ± 0.06 |
0.33 ± 0.06 |
0.46 ± 0.04 |
0.46 ± 0.04 |
0.44 ± 0.03 |
0.39 ± 0.05 |
|
|
Overall error rate |
0.18 ± 0.01 |
0.23 ± 0.01 |
0.23 ± 0.01 |
0.18 ± 0.01 |
0.18 ± 0.01 |
0.19 ± 0.01 |
0.21 ± 0.00 |
|
|
Effect error rate |
0.27 ± 0.05 |
0.40 ± 0.04 |
0.40 ± 0.04 |
0.20 ± 0.06 |
0.20 ± 0.06 |
0.18 ± 0.09 |
0.36 ± 0.05 |
|
|
No effect error rate |
0.16 ± 0.02 |
0.19 ± 0.02 |
0.19 ± 0.02 |
0.18 ± 0.02 |
0.18 ± 0.02 |
0.19 ± 0.03 |
0.18 ± 0.03 |
|
|
sensitivity |
0.47 ± 0.10 |
0.36 ± 0.12 |
0.36 ± 0.12 |
0.37 ± 0.08 |
0.38 ± 0.08 |
0.34 ± 0.12 |
0.41 ± 0.13 |
|
|
specificity |
0.93 ± 0.03 |
0.92 ± 0.04 |
0.92 ± 0.04 |
0.96 ± 0.02 |
0.96 ± 0.02 |
0.97 ± 0.04 |
0.92 ± 0.04 |
|
|
|
||||||||
|
lysozyme |
AUC |
0.83 ± 0.02 |
0.68 ± 0.04 |
0.68 ± 0.05 |
0.81 ± 0.04 |
0.81 ± 0.04 |
0.78 ± 0.04 |
0.77 ± 0.04 |
|
MCC |
0.40 ± 0.05 |
0.23 ± 0.06 |
0.23 ± 0.06 |
0.38 ± 0.08 |
0.38 ± 0.08 |
0.36 ± 0.11 |
0.28 ± 0.09 |
|
|
Overall error rate |
0.17 ± 0.02 |
0.24 ± 0.01 |
0.24 ± 0.02 |
0.17 ± 0.03 |
0.17 ± 0.03 |
0.16 ± 0.02 |
0.21 ± 0.03 |
|
|
Effect error rate |
0.40 ± 0.05 |
0.63 ± 0.05 |
0.63 ± 0.05 |
0.39 ± 0.12 |
0.39 ± 0.12 |
0.33 ± 0.13 |
0.54 ± 0.09 |
|
|
No effect error rate |
0.13 ± 0.02 |
0.15 ± 0.01 |
0.15 ± 0.01 |
0.13 ± 0.03 |
0.13 ± 0.03 |
0.15 ± 0.02 |
0.14 ± 0.02 |
|
|
Sensitivity |
0.43 ± 0.11 |
0.39 ± 0.07 |
0.39 ± 0.07 |
0.38 ± 0.17 |
0.38 ± 0.17 |
0.28 ± 0.09 |
0.36 ± 0.11 |
|
|
Specificity |
0.93 ± 0.03 |
0.84 ± 0.02 |
0.84 ± 0.02 |
0.93 ± 0.07 |
0.93 ± 0.07 |
0.97 ± 0.01 |
0.89 ± 0.04 |
|
|
|
||||||||
|
Train: lac rep |
AUC |
0.80 |
0.66 |
0.67 |
0.78 |
0.78 |
0.77 |
0.77 |
|
MCC |
0.40 |
0.23 |
0.23 |
0.35 |
0.35 |
0.35 |
0.35 |
|
|
Overall error rate |
0.20 |
0.27 |
0.24 |
0.17 |
0.17 |
0.16 |
0.16 |
|
|
Test: lysozyme |
Effect error rate |
0.52 |
0.65 |
0.63 |
0.41 |
0.41 |
0.32 |
0.32 |
|
No effect error rate |
0.10 |
0.14 |
0.15 |
0.14 |
0.14 |
0.15 |
0.16 |
|
|
Sensitivity |
0.58 |
0.46 |
0.39 |
0.33 |
0.33 |
0.26 |
0.26 |
|
|
Specificity |
0.85 |
0.80 |
0.84 |
0.95 |
0.95 |
0.97 |
0.97 |
|
|
|
||||||||
|
Train: lysozyme |
AUC |
0.81 |
0.71 |
0.71 |
0.80 |
0.80 |
0.79 |
0.79 |
|
MCC |
0.43 |
0.37 |
0.37 |
0.41 |
0.41 |
0.42 |
0.42 |
|
|
Overall error rate |
0.20 |
0.22 |
0.22 |
0.20 |
0.20 |
0.19 |
0.19 |
|
|
Test: lac rep |
Effect error rate |
0.34 |
0.43 |
0.43 |
0.25 |
0.25 |
0.18 |
0.18 |
|
No effect error rate |
0.17 |
0.17 |
0.17 |
0.19 |
0.19 |
0.20 |
0.20 |
|
|
Sensitivity |
0.45 |
0.46 |
0.46 |
0.33 |
0.33 |
0.30 |
0.30 |
|
|
Specificity |
0.92 |
0.88 |
0.88 |
0.96 |
0.96 |
0.98 |
0.98 |
|
|
|
||||||||
|
Column: (1) trained on all variables, tested with all variables observed; (2) trained on all variables, tested without any structural information (NoS) – only evolutionary variables observed; (3) trained and tested using only five evolutionary nodes; (4) trained on all variables, tested without any evolutionary information (NoE) – only structural variables observed; (5) trained and tested using only eight structural nodes; (6) trained on all variables, tested with only key variables observed (see later section); (7) trained and tested using only the three key variables. |
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|
Needham et al. BMC Bioinformatics 2006 7:405 doi:10.1186/1471-2105-7-405 |
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