Immunome Research

Table 4 Five-fold cross-validation performance of the pan-specific NetMHCIIpan-2.0 method compared to the allele-specific NN-align and TEPITOPE methods on the quantitative benchmark data set

From: NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure

			*NN-align*		*NetMHCIIpan-2.0*		*TEPITOPE*
Allele	#	# bind	PCC	AUC	PCC	AUC	AUC
DRB1*0101	7685	4382	0.675	0.825	0.711	0.846	0.727
DRB1*0301	2505	649	0.690	0.855	0.709	0.864	0.718
DRB1*0302	148	44	0.272	0.659	0.525	0.757
DRB1*0401	3116	1039	0.643	0.833	0.670	0.848	0.762
DRB1*0404	577	336	0.565	0.766	0.630	0.818	0.747
DRB1*0405	1582	627	0.710	0.869	0.698	0.858	0.780
DRB1*0701	1745	849	0.718	0.855	0.740	0.864	0.777
DRB1*0802	1520	431	0.518	0.778	0.526	0.780	0.645
DRB1*0806	118	91	0.744	0.902	0.796	0.924	0.884
DRB1*0813	1370	455	0.729	0.878	0.746	0.885	0.750
DRB1*0819	116	54	0.370	0.706	0.608	0.808
DRB1*0901	1520	622	0.597	0.810	0.634	0.818
DRB1*1101	1794	778	0.756	0.873	0.777	0.883	0.793
DRB1*1201	117	81	0.699	0.860	0.764	0.892
DRB1*1202	117	79	0.695	0.866	0.769	0.900
DRB1*1302	1580	493	0.630	0.819	0.634	0.825	0.596
DRB1*1402	118	78	0.623	0.825	0.694	0.860
DRB1*1404	30	16	0.466	0.661	0.613	0.737
DRB1*1412	116	63	0.680	0.857	0.757	0.894
DRB1*1501	1769	709	0.641	0.815	0.653	0.819	0.731
DRB3*0101	1501	281	0.673	0.843	0.690	0.850
DRB3*0301	160	70	0.604	0.826	0.736	0.853
DRB4*0101	1521	485	0.701	0.854	0.675	0.837
DRB5*0101	3106	1280	0.735	0.865	0.765	0.882	0.760
Ave	33931	13992	0.631	0.821	0.688	0.846
Ave*			0.673	0.841	0.697	0.854	0.744
Ave**			0.580	0.797	0.679	0.837

# gives the number of peptide binding data for each allele, #bind gives the number of peptides with a binding affinity stronger than 500 nM. NN-align is the method described by Nielsen et al. [5], NetMHCIIpan-2.0 is the method described here, and TEPITOPE is the method described by Sturniolo et al. [1]. Ave gives the per allele average, Ave* gives the per allele average of the 13 alleles characterized by the TEPITOPE method, and Ave** gives the per allele average of the 11 allele not characterized by the TEPITOPE method. In bold is highlighted the best performing method for each of the 24 alleles. AUC values were calculated using a binding threshold of 500 nM. Only AUC values are included for the TEPITOPE method since prediction values for this method are not linearly related to the binding affinity.

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