EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information

Saethang, Thammakorn; Hirose, Osamu; Kimkong, Ingorn; Tran, Vu Anh; Dang, Xuan Tho; Nguyen, Lan Anh T; Le, Tu Kien T; Kubo, Mamoru; Yamada, Yoichi; Satou, Kenji

doi:10.1186/1471-2105-13-313

Table 3 Classification results of 34 allele datasets

From: EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information

MHC	# of peptides	AUC
MHC	# of peptides	ARB	SMM	SMM^PMBEC	NetMHC	EpicCapo	EpicCapo⁺
HLA-A*01:01	1157	0.964	0.980	0.977	0.982	0.972 ± 0.004	0.977 ± 0.003
HLA-A*02:01	3089	0.934	0.952	0.946	0.957	0.950 ± 0.004	0.951 ± 0.004
HLA-A*02:02	1447	0.875	0.899	0.899	0.900	0.901 ± 0.004	0.909 ± 0.004
HLA-A*02:03	1443	0.884	0.916	0.916	0.921	0.920 ± 0.003	0.923 ± 0.003
HLA-A*02:06	1437	0.872	0.914	0.916	0.927	0.925 ± 0.004	0.927 ± 0.004
HLA-A*03:01	2094	0.908	0.940	0.928	0.937	0.934 ± 0.004	0.938 ± 0.003
HLA-A*11:01	1985	0.918	0.948	0.939	0.951	0.945 ± 0.004	0.951 ± 0.002
HLA-A*24:02	197	0.718	0.780	0.801	0.825	0.853 ± 0.012	0.865 ± 0.011
HLA-A*26:01	672	0.907	0.931	0.924	0.956	0.941 ± 0.005	0.957 ± 0.007
HLA-A*29:02	160	0.755	0.911	0.916	0.935	0.944 ± 0.008	0.945 ± 0.010
HLA-A*31:01	1869	0.909	0.930	0.925	0.928	0.930 ± 0.002	0.935 ± 0.003
HLA-A*33:01	1140	0.892	0.925	0.925	0.915	0.926 ± 0.004	0.934 ± 0.004
HLA-A*68:01	1141	0.840	0.885	0.885	0.883	0.891 ± 0.003	0.899 ± 0.003
HLA-A*68:02	1434	0.865	0.898	0.889	0.899	0.901 ± 0.005	0.907 ± 0.003
HLA-B*07:02	1262	0.952	0.964	0.960	0.965	0.960 ± 0.004	0.964 ± 0.002
HLA-B*08:01	708	0.936	0.943	0.956	0.955	0.942 ± 0.005	0.951 ± 0.004
HLA-B*15:01	978	0.900	0.952	0.940	0.941	0.940 ± 0.006	0.950 ± 0.005
HLA-B*18:01	118	0.573	0.853	0.880	0.838	0.886 ± 0.013	0.911 ± 0.009
HLA-B*27:05	969	0.915	0.940	0.941	0.938	0.949 ± 0.005	0.958 ± 0.003
HLA-B*35:01	736	0.851	0.889	0.889	0.875	0.900 ± 0.004	0.907 ± 0.007
HLA-B*40:02	118	0.541	0.842	0.843	0.754	0.811 ± 0.007	0.912 ± 0.011
HLA-B*44:02	119	0.533	0.740	0.739	0.778	0.798 ± 0.009	0.861 ± 0.013
HLA-B*44:03	119	0.461	0.770	0.753	0.763	0.813 ± 0.010	0.871 ± 0.008
HLA-B*51:01	244	0.822	0.868	0.895	0.886	0.930 ± 0.012	0.948 ± 0.015
HLA-B*53:01	254	0.871	0.882	0.885	0.899	0.916 ± 0.008	0.940 ± 0.008
HLA-B*54:01	255	0.847	0.921	0.935	0.903	0.927 ± 0.008	0.938 ± 0.006
HLA-B*57:01	59	0.428	0.871	0.843	0.826	0.792 ± 0.009	0.854 ± 0.010
HLA-B*58:01	988	0.889	0.964	0.945	0.961	0.959 ± 0.005	0.964 ± 0.004
H-2 Db	303	0.865	0.912	0.901	0.933	0.940 ± 0.014	0.968 ± 0.006
H-2 Dd	85	0.696	0.853	0.837	0.925	0.956 ± 0.016	0.985 ± 0.017
H-2 Kb	223	0.792	0.810	0.833	0.850	0.844 ± 0.021	0.880 ± 0.017
H-2 Kd	176	0.798	0.936	0.931	0.939	0.950 ± 0.015	0.966 ± 0.009
H-2 Kk	164	0.758	0.770	0.793	0.790	0.883 ± 0.009	0.926 ± 0.008
H-2 Ld	102	0.551	0.924	0.942	0.977	0.984 ± 0.012	0.992 ± 0.013
Average		0.801	0.895	0.895	0.900	0.912	0.931
t-test\|ARB		NA	4.37E-5	3.69E-5	1.25E-5	5.21E-6	2.64E-6
t-test\|SMM			NA	8.61E-1	2.30E-1	8.28E-3	2.87E-5
t-test\|SMM^PMBEC				NA	2.61E-1	3.50E-3	8.49E-6
t-test\|NetMHC					NA	8.57E-3	7.74E-5
t-test\|EpicCapo						NA	1.95E-5

For each dataset, AUCs were evaluated based on 5-fold cross validation. In the lower part, p-values of average AUCs were calculated using paired t-tests (two-tailed).
Means and standard deviations were calculated by 20 iterations of 5-fold cross validation for EpicCapo and EpicCapo⁺.
Underlined values represent the highest performance among ARB, SMM, SMM^PMBEC, and NetMHC. Values in bold represent significant improvements of EpicCapo or EpicCapo⁺ AUCs from 20 iterations of 5-fold cross validation over the underlined values according to t-tests (one-tailed, significance level = 0.01).

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