EFigure 1. A semi-screenshot to show the top page of the iSMP-Grey

EFigure 1. A semi-screenshot to show the top page of the iSMP-Grey web-server. Its web-site address is at http://www.jci-bioinfo.cn/iSMPGrey. doi:10.1371/journal.pone.0049040.g8 z z > TP N {m > > < TN N { {m{ > FP m{ > > : FN mz?7?It follows by substituting Eq.17 into Eq.16 and noting Eq.15 8 z > Sn 1{ m > > > Nz > > { > > > Sp 1{ m > > > N{ > > < mz zm{ Acc L 1{ z > N zN { > > z > > m m{ > 1{ N z z N { > > > > MCC r ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi > > > { {mz z {m{ > : 1z m N { 1z m N z?8?have the overall accuracy Acc L 1; while mz N z and m{ N { meaning that all the Iloperidone metabolite Hydroxy Iloperidone secreted proteins in the I-BRD9 dataset z and all the non-secreted proteins in { were incorrectly predicted, we have the overall accuracy Acc L 0. The MCC correlation coefficient is usually used for measuring the quality of binary (two-class) classifications. When mz m{ 0 meaning that none of the secreted proteins in the dataset z and none of the non-secreted proteins in { was incorrectly predicted, we have Mcc 1; when mz N z =2 and m{ N { =2 we have Mcc 0 meaning no better than random prediction; when mz N z and m{ N { we have MCC {1 meaning total disagreement between prediction and observation. As we can see from the above discussion, it is much more intuitive and easier-tounderstand when using Eq.18 to examine a predictor for its sensitivity, specificity, overall accuracy, and Mathew’s correlation coefficient.Results and DiscussionThe results obtained with iSMP-Grey on the benchmark dataset Bench of Eq.1 by the jackknife test are given in Table 1, where for facilitating comparison the results obtained by the KMID predictor [4] on the same benchmark dataset with the same test method are also given. As we can see from Table 1, the overall success rate by iSMP-Grey was 94.84 with MCC 0:90, which are remarkably higher than those by the KMID predictor [4]. Moreover, a comparison was also made with the PSEApred predictor [2]. Although the results by PSEApred as reported by Verma et al. [2] were also based on the same benchmark dataset P Bench of Eq.1, the test method used by these authors for PSEApred was 5-fold cross-validation. As elaborated in [34], this would make the test without a unique result as demonstrated below. For the current case, Bench consists of z and { , whereAs can be 18325633 obviously seen from the above equation, when mz 0 meaning none of the secreted proteins was missed in prediction, we have the sensitivity Sn 1; while mz N z meaning all the secreted proteins were missed in prediction, we have the sensitivity Sn 0. Likewise, when m{ 0 meaning none of the non-secreted proteins was incorrectly predicted as secreted protein, we have the specificity Sp 1; while m{ N { meaning all the non-secreted proteins were incorrectly predicted as secreted proteins, we have the specificity Sp 0. When mz m{ 0 meaning that none of the secreted proteins in the dataset z and non of non-secreted proteins in { was incorrectly predicted, wePredicting Secretory Proteins of Malaria Parasitez contains 252 secretory proteins of malaria parasite, and { contains 252 non-secretory proteins of malaria parasite. Substituting these data into Eqs.28?9 of [34] with M 2 (number of groups for classification) and C 5 (number of folds for crossvalidation), we obtainTable 2. A comparison between iSMP-Grey and PSEApred by 5-fold cross-validatio.EFigure 1. A semi-screenshot to show the top page of the iSMP-Grey web-server. Its web-site address is at http://www.jci-bioinfo.cn/iSMPGrey. doi:10.1371/journal.pone.0049040.g8 z z > TP N {m > > < TN N { {m{ > FP m{ > > : FN mz?7?It follows by substituting Eq.17 into Eq.16 and noting Eq.15 8 z > Sn 1{ m > > > Nz > > { > > > Sp 1{ m > > > N{ > > < mz zm{ Acc L 1{ z > N zN { > > z > > m m{ > 1{ N z z N { > > > > MCC r ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi > > > { {mz z {m{ > : 1z m N { 1z m N z?8?have the overall accuracy Acc L 1; while mz N z and m{ N { meaning that all the secreted proteins in the dataset z and all the non-secreted proteins in { were incorrectly predicted, we have the overall accuracy Acc L 0. The MCC correlation coefficient is usually used for measuring the quality of binary (two-class) classifications. When mz m{ 0 meaning that none of the secreted proteins in the dataset z and none of the non-secreted proteins in { was incorrectly predicted, we have Mcc 1; when mz N z =2 and m{ N { =2 we have Mcc 0 meaning no better than random prediction; when mz N z and m{ N { we have MCC {1 meaning total disagreement between prediction and observation. As we can see from the above discussion, it is much more intuitive and easier-tounderstand when using Eq.18 to examine a predictor for its sensitivity, specificity, overall accuracy, and Mathew’s correlation coefficient.Results and DiscussionThe results obtained with iSMP-Grey on the benchmark dataset Bench of Eq.1 by the jackknife test are given in Table 1, where for facilitating comparison the results obtained by the KMID predictor [4] on the same benchmark dataset with the same test method are also given. As we can see from Table 1, the overall success rate by iSMP-Grey was 94.84 with MCC 0:90, which are remarkably higher than those by the KMID predictor [4]. Moreover, a comparison was also made with the PSEApred predictor [2]. Although the results by PSEApred as reported by Verma et al. [2] were also based on the same benchmark dataset P Bench of Eq.1, the test method used by these authors for PSEApred was 5-fold cross-validation. As elaborated in [34], this would make the test without a unique result as demonstrated below. For the current case, Bench consists of z and { , whereAs can be 18325633 obviously seen from the above equation, when mz 0 meaning none of the secreted proteins was missed in prediction, we have the sensitivity Sn 1; while mz N z meaning all the secreted proteins were missed in prediction, we have the sensitivity Sn 0. Likewise, when m{ 0 meaning none of the non-secreted proteins was incorrectly predicted as secreted protein, we have the specificity Sp 1; while m{ N { meaning all the non-secreted proteins were incorrectly predicted as secreted proteins, we have the specificity Sp 0. When mz m{ 0 meaning that none of the secreted proteins in the dataset z and non of non-secreted proteins in { was incorrectly predicted, wePredicting Secretory Proteins of Malaria Parasitez contains 252 secretory proteins of malaria parasite, and { contains 252 non-secretory proteins of malaria parasite. Substituting these data into Eqs.28?9 of [34] with M 2 (number of groups for classification) and C 5 (number of folds for crossvalidation), we obtainTable 2. A comparison between iSMP-Grey and PSEApred by 5-fold cross-validatio.

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