Predicting the functions of a protein from its ability to associate with other molecules

Taha, Kamal; Yoo, Paul D.

doi:10.1186/s12859-016-0882-3

BMC Bioinformatics

Table 7 Performance of predicting the molecular function annotations using randomly selected sets of training and testing proteins

From: Predicting the functions of a protein from its ability to associate with other molecules

GO Term	Average depth (level) of GO term	Number of training proteins	Number of testing proteins	PPFBM			GOstruct			Text-KNN
GO Term	Average depth (level) of GO term	Number of training proteins	Number of testing proteins	R	P	F	R	P	F	R	P	F
GO:0038023	4	830	210	0.62	0.67	0.55	0.41	0.43	0.53	0.25	0.33	0.28
GO:0009927	4	51	15	0.42	0.46	0.44	0.53	0.56	0.54	0.00	0.00	0.00
GO:0000156	4	1399	350	0.78	0.79	0.78	0.37	0.44	0.40	0.37	0.46	0.41
GO:0005057	4	1014	250	0.59	0.64	0.61	0.40	0.43	0.41	0.35	0.43	0.39
GO:0004888	5	580	140	0.60	0.64	0.62	0.43	0.48	0.45	0.24	0.29	0.26
GO:0015026	5	109	20	0.46	0.54	0.50	0.45	0.49	0.47	0.21	0.29	0.24
GO:0005220	5	42	8	0.37	0.42	0.39	0.49	0.56	0.52	0.18	0.31	0.23
GO:0030594	5	546	130	0.78	0.79	0.78	0.48	0.50	0.49	0.30	0.43	0.35
GO:0000155	5	1034	250	0.81	0.84	0.82	0.42	0.46	0.44	0.39	0.42	0.40
GO:0009881	5	289	70	0.61	0.66	0.55	0.45	0.48	0.46	0.29	0.37	0.33
GO:0008329	5	136	30	0.50	0.55	0.52	0.43	0.46	0.44	0.15	0.30	0.20
GO:0004887	5	81	20	0.44	0.53	0.48	0.46	0.59	0.52	0.09	0.16	0.12
GO:0003707	5	878	220	0.59	0.68	0.63	0.38	0.41	0.39	0.23	0.32	0.27
GO:0004896	6	130	35	0.52	0.52	0.52	0.45	0.48	0.46	0.26	0.32	0.29
GO:0016502	6	169	45	0.56	0.57	0.56	0.47	0.49	0.48	0.25	0.31	0.28
GO:0005035	6	51	10	0.46	0.48	0.47	0.51	0.53	0.52	0.00	0.00	0.00
GO:0016917	6	198	50	0.55	0.63	0.59	0.46	0.48	0.47	0.30	0.38	0.34
GO:0008066	6	301	80	0.56	0.63	0.59	0.43	0.46	0.44	0.32	0.39	0.35
GO:0008158	6	138	35	0.49	0.56	0.52	0.46	0.51	0.48	0.25	0.35	0.29
GO:0008046	6	58	15	0.44	0.45	0.44	0.47	0.55	0.51	0.00	0.00	0.00
GO:0004984	6	3474	870	0.84	0.87	0.85	0.33	0.39	0.35	0.33	0.41	0.37
GO:0035586	6	207	55	0.54	0.65	0.59	0.44	0.46	0.45	0.31	0.40	0.35
GO:0017154	6	82	20	0.51	0.59	0.56	0.47	0.56	0.51	0.16	0.20	0.18
GO:0019199	6	756	190	0.56	0.60	0.58	0.37	0.41	0.55	0.28	0.40	0.33
GO:0042813	6	141	40	0.48	0.53	0.50	0.43	0.46	0.44	0.29	0.32	0.30
GO:0004915	7	111	30	0.44	0.47	0.45	0.38	0.43	0.40	0.19	0.27	0.22
GO:0004908	7	35	10	0.38	0.39	0.38	0.54	0.57	0.55	0.17	0.29	0.21
GO:0004950	7	210	50	0.55	0.58	0.56	0.44	0.42	0.42	0.28	0.42	0.34
GO:0004897	7	29	7	0.41	0.42	0.41	0.56	0.58	0.67	0.19	0.34	0.24
GO:0004904	7	176	45	0.55	0.56	0.55	0.42	0.43	0.42	0.26	0.35	0.30

The table shows the average depth (level) of each GO term in the molecular function subontology and the accuracy of predicting the function of this term. R, P, and F DENOTE Recall, Precision, and F-value respectively

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