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

Table 1 Performance of ExportPred variants

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

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.

ISSN: 1474-760X