TABLE 1.

Correlation of the in silico analysis data with experimental data of cross-reactivity.

		MHC binding affinity			Ranks (%) of being presented	Experimental data
Epitope	Peptide Sq	NetMHC 4.0		IEDB	NetCTLpan	[Peptide] (μg/ml)
		Affinity (nM)	Rank (%)	Rank (%)		1.0	0.01
AFP158	FMNKFIYEI	3.2	0.01	0.2	0.01	++++	++++
ENPP1436	YLNKYLGDV	28.67	0.4	0.6	1	+++	+
RCL1215	ILNKFIPDI	64.06	0.8	2	0.8	−/−/++	−/−/+
FL2D189	LQKKYSEEL	11170.64	17	22	6	+/+/++	−/−/−
EPG51033	SIEKFCAEG	20847.93	29	37	50	−/−/+	−/−/−

The peptide’s HLA-A2 binding affinity is analyzed by NetMHC4.0 and IEDB software. The likelihood (rank) of the peptides being processed and presented by MHC molecules is analyzed by NetCTLpan program. The lower the number, the higher the chance of that peptide being processed and presented. The rank of NetMHC4.0 binding affinity is based on 400,000 random natural peptides. The ranks of the peptide being processed and presented is based on 200,000 random natural peptides. The wet laboratory experimental data of cross reactivity is shown in the last column. In the last column where the reactivity is different among TCR1, 2, and 3, their reactivity is indicated as TCR1/TCR2/TCR3.