Empirically estimated Sensitivity (Sen), Positive predictive value (PPV) and F-score (harmonic average of Sen and PPV) achieved by CoreBoost_HM at different threshold. The prediction results were clustered using a window of size 1 kb. All these results were estimated on training set (2.4 kb long regions) by ten fold cross validation.
Sen = TP/(FP +FN),
PPV=TP/(TP+FP),
F=2*Sen*PPV/(Sen+PPV),
TP is the true positives, TN is the true negatives, FP is the false positives and FN is the false negatives.
|
Threshold |
CpG related promoter |
non-CpG related promoter |
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|
Resolution |
Resolution |
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|
50 bp |
200 bp |
500 bp |
50 bp |
200 bp |
500 bp |
|||||||||||||
|
Sen |
PPV |
F |
Sen |
PPV |
F |
Sen |
PPV |
F |
Sen |
PPV |
F |
Sen |
PPV |
F |
Sen |
PPV |
F |
|
|
0.5 |
0.58 |
0.59 |
0.58 |
0.78 |
0.79 |
0.79 |
0.91 |
0.93 |
0.92 |
0.39 |
0.39 |
0.39 |
0.56 |
0.56 |
0.56 |
0.71 |
0.71 |
0.71 |
|
0.6 |
0.57 |
0.59 |
0.58 |
0.77 |
0.80 |
0.78 |
0.90 |
0.93 |
0.91 |
0.38 |
0.41 |
0.39 |
0.54 |
0.58 |
0.56 |
0.67 |
0.73 |
0.70 |
|
0.7 |
0.57 |
0.60 |
0.59 |
0.76 |
0.80 |
0.78 |
0.88 |
0.93 |
0.91 |
0.37 |
0.43 |
0.40 |
0.52 |
0.60 |
0.56 |
0.64 |
0.75 |
0.69 |
|
0.85 |
0.56 |
0.60 |
0.58 |
0.75 |
0.81 |
0.78 |
0.87 |
0.94 |
0.90 |
0.34 |
0.45 |
0.39 |
0.48 |
0.63 |
0.54 |
0.59 |
0.77 |
0.67 |
|
1 |
0.55 |
0.61 |
0.58 |
0.74 |
0.82 |
0.78 |
0.84 |
0.94 |
0.89 |
0.32 |
0.48 |
0.38 |
0.45 |
0.66 |
0.53 |
0.54 |
0.80 |
0.65 |
|
2 |
0.48 |
0.66 |
0.55 |
0.62 |
0.86 |
0.72 |
0.70 |
0.96 |
0.80 |
0.20 |
0.59 |
0.30 |
0.26 |
0.79 |
0.39 |
0.30 |
0.91 |
0.46 |
|
3 |
0.39 |
0.70 |
0.50 |
0.50 |
0.90 |
0.64 |
0.55 |
0.98 |
0.70 |
0.12 |
0.66 |
0.20 |
0.15 |
0.85 |
0.26 |
0.17 |
0.94 |
0.28 |
|
5 |
0.21 |
0.78 |
0.33 |
0.25 |
0.94 |
0.40 |
0.27 |
0.99 |
0.42 |
0.04 |
0.83 |
0.08 |
0.05 |
0.93 |
0.09 |
0.05 |
0.97 |
0.09 |