Table 5.

Prediction performance on singular peptide set (SP) using training sets with and without homologs.

Allelic variant	SR AUC	ALL AUC	AUC reduction1	# peptide reduction2	% peptide reduction3
HLA-DPA1*0103-DPB1*0201	0.787	0.797	0.010	801	0.571
HLA-DPA1*01-DPB1*0401	0.809	0.801	-0.008	797	0.596
HLA-DPA1*0201-DPB1*0101	0.764	0.735	-0.029	795	0.568
HLA-DPA1*0201-DPB1*0501	0.587	0.640	0.053	824	0.584
HLA-DPA1*0301-DPB1*0402	0.744	0.772	0.028	805	0.572
HLA-DQA1*0101-DQB1*0501	0.850	0.821	-0.029	1155	0.664
HLA-DQA1*0102-DQB1*0602	0.667	0.719	0.052	1036	0.636
HLA-DQA1*0301-DQB1*0302	0.569	0.756	0.187	1123	0.653
HLA-DQA1*0401-DQB1*0402	0.632	0.551	-0.081	1116	0.656
HLA-DQA1*0501-DQB1*0201	0.587	0.652	0.065	1069	0.645
HLA-DQA1*0501-DQB1*0301	0.764	0.766	0.002	1087	0.644
HLA-DRB1*0101	0.777	0.781	0.004	2923	0.455
HLA-DRB1*0301	0.782	0.786	0.004	579	0.338
HLA-DRB1*0401	0.682	0.709	0.027	548	0.310
HLA-DRB1*0404	0.805	0.818	0.013	103	0.179
HLA-DRB1*0405	0.765	0.748	-0.017	533	0.337
HLA-DRB1*0701	0.793	0.810	0.017	570	0.327
HLA-DRB1*0802	0.672	0.622	-0.050	503	0.331
HLA-DRB1*0901	0.669	0.651	-0.018	478	0.314
HLA-DRB1*1101	0.809	0.799	-0.010	590	0.329
HLA-DRB1*1302	0.712	0.733	0.021	510	0.323
HLA-DRB1*1501	0.712	0.719	0.007	598	0.338
HLA-DRB3*0101	0.829	0.838	0.009	514	0.342
HLA-DRB4*0101	0.762	0.745	-0.017	510	0.335
HLA-DRB5*0101	0.774	0.798	0.024	571	0.323
H-2-IAb	0.816	0.833	0.017	114	0.173
Average	0.737	0.748	0.011	779	0.444

The "ALL" column indicates 5-fold cross validation performance of this subset trained with entire dataset. The "SR" indicates 5-fold cross validation performance of this subset trained with sequence similarity reduced dataset.

1. AUC reduction = AUC all - AUC SR

2. # peptide reduction = # peptide all - # peptide SR

3. % peptide reduction = (# peptide all - # peptide SR)/# peptide all