Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences

Table 6 Prediction performance of consensus methods that combine two or three methods

Results on the yeast data
	Full model	M2-M3-M4	M1-M3-M4	M1-M2-M4	M1-M2-M3	M1-M2	M1-M3	M1-M4	M2-M3	M2-M4	M3-M4
AUC	0.85	0.81	0.85	0.85	0.85	0.85	0.85	0.85	0.79	0.81	0.81
P20R	0.34	0.37	0.34	0.35	0.29	0.29	0.29	0.35	0.32	0.38	0.37
Results on the human data
	Full model	M2-M3-M4	M1-M3-M4	M1-M2-M4	M1-M2-M3	M1-M2	M1-M3	M1-M4	M2-M3	M2-M4	M3-M4
AUC	0.90	0.88	0.90	0.90	0.89	0.89	0.89	0.90	0.82	0.88	0.88
P20R	0.67	0.63	0.67	0.67	0.64	0.64	0.64	0.67	0.52	0.62	0.63
Results on the combined data
	Full model	M2-M3-M4	M1-M3-M4	M1-M2-M4	M1-M2-M3	M1-M2	M1-M3	M1-M4	M2-M3	M2-M4	M3-M4
AUC	0.88	0.86	0.88	0.88	0.86	0.86	0.86	0.88	0.81	0.86	0.86
P20R	0.59	0.54	0.59	0.59	0.54	0.54	0.54	0.59	0.48	0.54	0.54
Results on the cross-species testing, Human - Yeast ¹
	Full model	M2-M3-M4	M1-M3-M4	M1-M2-M4	M1-M2-M3	M1-M2	M1-M3	M1-M4	M2-M3	M2-M4	M3-M4
AUC	0.73	0.71	0.73	0.73	0.73	0.73	0.73	0.73	0.72	0.71	0.71
P20R	0.07	0.07	0.07	0.07	0.06	0.06	0.06	0.07	0.06	0.07	0.07
Results on the cross-species testing, Yeast - Human ¹
	Full model	M2-M3-M4	M1-M3-M4	M1-M2-M4	M1-M2-M3	M1-M2	M1-M3	M1-M4	M2-M3	M2-M4	M3-M4
AUC	0.68	0.65	0.68	0.68	0.67	0.67	0.67	0.68	0.67	0.65	0.65
P20R	0.04	0.03	0.04	0.04	0.03	0.03	0.03	0.04	0.04	0.03	0.03

ISSN: 1471-2105