PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment

BMC Research Notes

Table 1 Prediction results of the test sets for five organisms with probability threshold of 0.5.

A. For *Human* PPI prediction
Test set	Sensitivity (%)	Specificity (%)	Accuracy (%)
1	88.91	92.13	90.67
2	89.05	92.48	90.76
3	89.34	92.03	90.69
4	89.24	92.42	90.83
5	89.28	91.49	90.39
Average	89.17	92.17	90.67 ± 0.17
B. For *Yeast* PPI prediction
Test set	Sensitivity (%)	Specificity (%)	Accuracy (%)
1	87.89	89.19	88.54
2	88.14	89.78	88.96
3	89.36	89.15	89.26
4	86.84	89.40	88.12
5	88.65	91.55	90.10
Average	88.17	89.81	88.99 ± 0.75
C. For *Drosophila* PPI prediction
Test set	Sensitivity (%)	Specificity (%)	Accuracy (%)
1	99.15	91.19	95.17
2	99.33	63.66	81.50
3	99.80	92.75	96.28
4	99.63	94.63	97.13
5	99.76	61.03	80.39
Average	99.53	80.65	90.09 ± 8.39
D. For *E.coli* PPI prediction
Test set	Sensitivity (%)	Specificity (%)	Accuracy (%)
1	91.27	97.87	94.55
2	96.55	91.55	94.05
3	93.42	96.87	95.15
4	98.49	71.28	84.88
5	95.83	94.18	95.00
Average	95.11	90.35	92.73 ± 3.94
E. For *C.elegans* PPI prediction
Test set	Sensitivity (%)	Specificity (%)	Accuracy (%)
1	97.02	98.20	97.91
2	96.53	98.76	97.33
3	96.34	99.13	97.74
4	96.34	98.33	97.33
5	96.09	98.33	97.21
Average	96.46	98.55	97.51 ± 0.22

With probability 0.5 as the threshold to assign class label, the prediction results of each species are shown in this table. For all species, the sensitivities are >88%, the specificities are >80% and the prediction accuracies are >88%. Moreover, each model gives a relatively low standard deviation (SD) of no more than 10%. So this method has a good robustness.

ISSN: 1756-0500