Predicting the effect of missense mutations on protein function: analysis with Bayesian networks

Needham, Chris J; Bradford, James R; Bulpitt, Andrew J; Care, Matthew A; Westhead, David R

doi:10.1186/1471-2105-7-405

BMC Bioinformatics

Table 3 Results with a learned Bayesian network.

From: Predicting the effect of missense mutations on protein function: analysis with Bayesian networks

Cross-validation	Trained on:	All	All	NoS	All	NoE	All	key
	Tested on:	All	NoS	NoS	NoE	NoE	key	key
mixed	AUC	0.84 ± 0.01	0.64 ± 0.01	0.70 ± 0.02	0.72 ± 0.02	0.82 ± 0.02	0.63 ± 0.03	0.80 ± 0.02
	MCC	0.46 ± 0.03	0.11 ± 0.03	0.10 ± 0.16	0.26 ± 0.22	0.44 ± 0.03	0.40 ± 0.04	0.40 ± 0.04
	Overall error rate	0.17 ± 0.01	0.67 ± 0.01	0.23 ± 0.00	0.36 ± 0.28	0.18 ± 0.01	0.18 ± 0.01	0.18 ± 0.01
	Effect error rate	0.27 ± 0.05	0.75 ± 0.01	0.15 ± 0.24	0.40 ± 0.25	0.29 ± 0.07	0.24 ± 0.06	0.25 ± 0.05
	No effect error rate	0.16 ± 0.01	0.11 ± 0.03	0.21 ± 0.03	0.29 ± 0.18	0.16 ± 0.02	0.18 ± 0.01	0.18 ± 0.01
	sensitivity	0.41 ± 0.07	0.93 ± 0.01	0.13 ± 0.21	0.51 ± 0.33	0.41 ± 0.08	0.31 ± 0.04	0.31 ± 0.09
	specificity	0.95 ± 0.02	0.15 ± 0.02	0.96 ± 0.07	0.68 ± 0.47	0.95 ± 0.03	0.97 ± 0.01	0.97 ± 0.01
lac rep	AUC	0.85 ± 0.01	0.47 ± 0.03	0.73 ± 0.02	0.70 ± 0.02	0.82 ± 0.02	0.61 ± 0.02	0.81 ± 0.02
	MCC	0.52 ± 0.02	0.11 ± 0.03	0.32 ± 0.04	0.43 ± 0.04	0.46 ± 0.05	0.42 ± 0.04	0.42 ± 0.03
	Overall error rate	0.17 ± 0.01	0.60 ± 0.01	0.24 ± 0.01	0.19 ± 0.01	0.18 ± 0.01	0.19 ± 0.01	0.19 ± 0.01
	Effect error rate	0.25 ± 0.03	0.72 ± 0.01	0.46 ± 0.03	0.20 ± 0.06	0.21 ± 0.05	0.17 ± 0.07	0.22 ± 0.06
	No effect error rate	0.15 ± 0.01	0.16 ± 0.02	0.19 ± 0.01	0.19 ± 0.01	0.18 ± 0.01	0.20 ± 0.01	0.19 ± 0.01
	sensitivity	0.51 ± 0.03	0.86 ± 0.02	0.40 ± 0.03	0.33 ± 0.03	0.38 ± 0.06	0.30 ± 0.02	0.33 ± 0.02
	specificity	0.94 ± 0.01	0.24 ± 0.02	0.88 ± 0.01	0.97 ± 0.01	0.96 ± 0.01	0.98 ± 0.01	0.97 ± 0.01
lysozyme	AUC	0.86 ± 0.02	0.51 ± 0.06	0.67 ± 0.05	0.78 ± 0.04	0.83 ± 0.05	0.70 ± 0.04	0.78 ± 0.05
	MCC	0.47 ± 0.06	0.09 ± 0.05	-	0.37 ± 0.10	0.40 ± 0.10	0.37 ± 0.12	0.34 ± 0.12
	Overall error rate	0.17 ± 0.03	0.75 ± 0.02	0.19 ± 0.00	0.16 ± 0.02	0.16 ± 0.02	0.16 ± 0.02	0.16 ± 0.02
	Effect error rate	0.38 ± 0.14	0.80 ± 0.01	-	0.30 ± 0.13	0.34 ± 0.11	0.32 ± 0.13	0.33 ± 0.14
	No effect error rate	0.10 ± 0.03	0.05 ± 0.08	0.19 ± 0.00	0.15 ± 0.02	0.14 ± 0.02	0.15 ± 0.02	0.15 ± 0.02
	Sensitivity	0.55 ± 0.19	0.98 ± 0.02	0.00 ± 0.00	0.29 ± 0.10	0.36 ± 0.09	0.30 ± 0.09	0.26 ± 0.09
	Specificity	0.90 ± 0.07	0.07 ± 0.02	1.00 ± 1.00	0.97 ± 0.02	0.95 ± 0.02	0.97 ± 0.01	0.97 ± 0.01
Train: lac rep	AUC	0.72	0.43	0.68	0.70	0.77	0.57	0.75
	MCC	0.30	-	0.23	0.21	0.36	0.34	0.35
	Overall error rate	0.17	0.19	0.27	0.21	0.17	0.17	0.17
Test: lysozyme	Effect error rate	0.33	-	0.65	0.57	0.41	0.35	0.35
	No effect error rate	0.16	0.19	0.14	0.16	0.14	0.15	0.15
	Sensitivity	0.20	0.00	0.46	0.25	0.35	0.26	0.26
	Specificity	0.98	1.00	0.80	0.92	0.94	0.97	0.97
Train: lysozyme	AUC	0.79	0.44	0.65	0.58	0.78	0.66	0.78
	MCC	0.41	-0.11	0.32	0.06	0.42	0.40	0.41
	Overall error rate	0.20	0.39	0.24	0.25	0.20	0.20	0.20
Test: lac rep	Effect error rate	0.22	0.84	0.46	0.30	0.26	0.23	0.23
	No effect error rate	0.19	0.28	0.19	0.25	0.19	0.20	0.19
	Sensitivity	0.32	0.13	0.40	0.01	0.35	0.30	0.33
	Specificity	0.97	0.78	0.88	1.00	0.96	0.97	0.97

See Table 2 for column details. Note that MCC score or effect rate cannot be shown if all mutations are predicted as 'no effect'.

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ISSN: 1471-2105

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