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Table 1 Performance of ExportPred variants

From: Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites

Model number 1 2 3 4
PEXEL WMM Default Default Hiller Hiller
Signal sequence model Default SignalP Default SignalP
Negative set Positive set: training sequences
   PfNegative 0.98 0.90 0.97 0.88
   Simulated 0.99 0.95 0.99 0.95
   Simulated (PfSS) 0.96 0.80 0.92 0.61
   Simulated (SpSS) 0.97 0.50 0.95 0.16
   Simulated (EPSS) 0.95 0.88 0.91 0.79
Negative set Positive set: Rifins + Stevors
   PfNegative 0.96 0.97 0.95 0.94
   Simulated 0.98 0.99 0.97 0.99
   Simulated (PfSS) 0.95 0.93 0.91 0.77
   Simulated (SpSS) 0.95 0.61 0.93 0.21
   Simulated (EPSS) 0.91 0.96 0.89 0.91
  1. Performance of ExportPred as measured by area under the respective ROC curve for combinations of model variant, and positive and negative dataset. For each pair of positive and negative sets, the best performing model is highlighted in bold. The four model variants are constructed by substituting ExportPred PEXEL weight model matrix (WMM) with the one published in [6,7] and/or by substituting the ExportPred signal sequence states with the HMM used in SignalP.