Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores

Salomon, Jesper; Flower, Darren R

doi:10.1186/1471-2105-7-501

BMC Bioinformatics

Table 5 Results of SKM on multiple MHC Class II alleles from MHCPEP

From: Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores

MHC Allele	Species	#Samp	β	Acc.	Spec.	Sens.	A_ROC	A_ROC50	MCC	A_OVER-ROC
HLA-DR1¹	Human	1346	0.04	0.9123	0.9153	0.9094	0.9712	0.8460	0.8247	0.0288
- *0101		474	0.06	0.8987	0.9114	0.8861	0.9673	0.8864	0.7977	0.0327
- *0102		12	0.005	0.8333	0.6667	1	0.9444	0.9444	0.7071	0.0556
HLA-DR2¹	Human	648	0.15	0.9059	0.9692	0.8426	0.9608	0.8701	0.8183	0.0392
- *0201		44	0.8	0.8864	0.9091	0.8636	0.9360	0.9360	0.7735	0.0640
HLA-DR3¹	Human	378	0.15	0.9101	0.9577	0.8624	0.9750	0.9216	0.8239	0.0250
- *0301		242	0.02	0.9339	0.9008	0.9669	0.9847	0.9676	0.8697	0.0153
HLA-DR4¹	Human	1742	0.125	0.9248	0.9460	0.9036	0.9749	0.8677	0.8504	0.0251
- *0401		910	0.125	0.8890	0.9187	0.8593	0.9521	0.7989	0.7794	0.0479
- *0402		240	0.07	0.9	0.925	0.875	0.9717	0.9365	0.8010	0.0282
HLA-DR5	Human	398	0.125	0.9171	0.9799	0.8542	0.9717	0.9166	0.8408	0.0283
HLA-DR6	Human	46	0.25	0.9348	1	0.8696	0.9981	0.9981	0.8771	0.0019
HLA-DR7	Human	528	0.1	0.9034	0.9659	0.8409	0.9696	0.8965	0.8132	0.0304
HLA-DR8	Human	160	0.06	0.8938	0.8625	0.925	0.9683	0.9505	0.7890	0.0317
HLA-DR9	Human	192	0.2	0.9375	0.9896	0.8854	0.9779	0.9575	0.8798	0.0221
HLA-DR10	Human	12	5	0.5833	0.6667	0.5	0.6389	0.6389	0.1690	0.3611
HLA-DR11	Human	590	0.03	0.9169	0.9390	0.8949	0.9615	0.8847	0.8347	0.0385
HLA-DR14	Human	126	1	0.9762	1	0.9524	0.9934	0.9917	0.9535	0.0066
HLA-DR17	Human	308	0.03	0.9448	0.9545	0.9351	0.9802	0.9579	0.8898	0.0198
HLA-DR53	Human	72	0.2	0.8889	1	0.7778	0.9931	0.9931	0.7977	0.0069
HLA-DP9	Human	90	0.2	0.9889	0.9778	1	1	1	0.9780	0
HLA-DPw4	Human	38	0.01	0.7895	0.8421	0.7368	0.9058	0.9058	0.5822	0.0942
HLA-DQ1	Human	78	0.02	0.8974	0.9231	0.8718	0.9579	0.9579	0.7959	0.0420
HLA-DQ2	Human	210	0.08	0.8952	0.9714	0.8190	0.9664	0.936	0.7998	0.0336
HLA-DQ4	Human	194	0.2	0.8866	0.8969	0.8763	0.9557	0.9188	0.7734	0.0443
Weighted average		363.12	0.120	0.9120	0.9390	0.8850	0.9687	0.8852	0.8263	0.0313

Evaluating performance on multiple alleles using 10-fold CV. Average scores shown underneath, weighted by number of samples.
¹All binders belonging to a group of alleles.

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