ROC analyses for five NES prediction methods.

<p>(<b>A</b>) ROC curve generated with artificial NES datasets. For the artificial NES sets, 163 positive and 60 negative experimentally verified NESs were used to plot the ROC curves for the traditional consensus-based prediction, NetNES, NESmapper, Wregex, and NESsential. The true positive rates (TPRs) and false positive rates (FPRs) for each tool were measured by changing the threshold scores for Wregex and NESmapper or the threshold probability values for NESsential. The curves for the NESmapper predictions with the optimized and unoptimized profiles are shown with solid lines with red circles and with dotted lines with orange triangles, respectively, those for Wregex with solid lines with green squares, and those for NESsential with solid lines with blue diamonds. The results for the traditional consensus-based prediction and NetNES are shown with green and blue asterisks, respectively. (<b>B</b>) ROC curve generated with ValidNES/Sp-test datasets. We measured the false positives by counting NESs called from regions other than the ranges corresponding to true NESs. To calculate the FPRs for the ValidNES and Sp-test datasets, only called NESs that matched the traditional consensus sequence were counted as false positives and divided by the number of sequences that matched the traditional consensus sequence in each dataset (841 for ValidNES and 231 for Sp-test). The mean FPRs for both datasets were used for the analysis. (<b>C</b>) ROC curve generated with the artificial NES and ValidNES/Sp-test datasets.