Prediction of HLA-A2-restricted CTL epitope specific to HCC by SYFPEITHI combined with polynomial method

Table 1 Coefficients for the polynomial method.

Res	Position
	1	2	3	4	5	6	7	8	9
A	-2.38	-3.22	-2.8	-2.66	-2.89	-2.7	-2.35	-3.07	-2.49
C	-2.94	-15	-2.58	-1.96	-3.29	-2.22	-2.97	-2.37	-15.0
D	-3.69	-15	-3.46	-2.71	-2.26	-2.63	-3.61	-3.03	-15.0
E	-3.64	-15	-3.51	-2.65	-3.39	-3.41	-3.21	-2.63	-15.0
F	-1.89	-15	-2.35	-2.5	-1.34	-2.43	-2.18	-1.71	-15.0
G	-2.32	-15	-3.04	-2.63	-2.56	-2.3	-3.13	-2.96	-15.0
H	-2.67	-15	-2.58	-2.58	-2.05	-3.32	-3.13	-2.16	-15.0
I	-1.65	-2.55	-2.8	-3.44	-2.74	-2.79	-2.2	-2.69	-2.1
K	-2.51	-15	-3.65	-2.93	-3.34	-3.77	-2.97	-3.27	-15
L	-2.32	-1.7	-2.09	-2.49	-2.71	-2.63	-2.62	-2.01	-2.74
M	-0.39	-1.39	-1.79	-3.01	-3.43	-1.38	-1.33	-0.97	-2.96
N	-3.12	-15	-3.31	-2.22	-2.36	-2.3	-3.14	-3.31	-15.0
P	-3.61	-15	-2.97	-2.64	-2.42	-2.31	-1.83	-2.42	-15.0
Q	-2.76	-15	-2.81	-2.63	-3.06	-2.84	-2.12	-3.05	-15.0
R	-1.92	-15	-3.41	-2.61	-3.05	-3.76	-3.43	-3.02	-15.0
S	-2.39	-15	-2.04	-2.12	-2.83	-3.04	-2.73	-2.02	-15.0
T	-2.89	-3.58	-2.6	-2.48	-2.17	-2.58	-2.67	-3.14	-3.7
V	-2.44	-2.64	-2.68	-3.29	-2.49	-2.25	-2.68	-2.8	-1.7
W	-0.14	-15	-1.01	-2.94	-1.77	-2.77	-2.85	-2.13	-15.0
Y	-1.46	-15	-1.67	-2.7	-1.92	-2.39	-1.35	-3.37	-15.0

Coefficients of the polynomial method. For each of the 20 amino acid residues, the amount they contribute to the polynomial score is shown (for all nine positions in which they may occur).

Table 2 HLA-A2 restricted epitope prediction results.

Antigens	AApos	Sequence	SYFPEITHI score	Polynomial score
MAGE-1 (MAG1)	194	F L I I V L V M I	27	-17.07
	38	L V L G T L E E V	26	-20.77
	278	K V L E Y V I K V	26	-21.23
	101	V I T K K V A D L	25	-24.23
	301	A L R E E E E G V	25	-24.81
	187	Q I M P K T G F L	24	-23.24
	93	I L E S L F R A V	23	-22.32
	105	K V A D L V G F L	23	-23.12
	15	A L E A Q Q E A L	22	-25.17
	89	S T S C I L E S L	22	-23.31
MAGE-3 (MAG3)	108	A L S R K V A E L	31	-22.04
	201	L L I I V L A I I	28	-22.52
	200	G L L I I V L A I	27	-22.33
	271	F L W G P R A L V	27	-19.47
	220	K I W E E L S V L	26	-23.01
	112	K V A E L V H F L	25	-23.14
	237	S I L G D P K K L	25	-22.73
	176	Y I F A T C L G L	23	-21.73
	238	I L G D P K K L L	23	-23.01
	174	H L Y I F A T C L	22	-21.3
MAGE-8 (MAG8)	111	A L D E K V A E L	33	-23.5
	45	L I M G T L E E V	29	-21.63
	204	L L I I V L G M I	26	-21.58
	115	K V A E L V R F L	24	-23.44
	179	Y I L V T C L G L	24	-22.1
	71	S L T V T D S T L	23	-23.39
	203	G L L I I V L G M	23	-23.08
	205	L I I V L G M I L	23	-22.73
	20	G E A P G L M D V	21	-34.01
	25	L M D V Q I P T A	21	-23.75
P53 (P53)	24	K L L P E N N V L	26	-23.31
	187	G L A P P Q H L I	25	-21.96
	264	L L G R N S F E V	24	-21.58
	129	A L N K M F C Q L	23	-24.94
	132	K M F C Q L A K T	22	-23.22
	193	H L I R V E G N L	22	-24.86
	65	R M P E A A P P V	21	-20.47
	322	P L D G E Y F T L	21	-25.24
	256	T L E D S S G N L	20	-25.86
	113	F L H S G T A K S	19	-34.05
AFP (FETA)	90	Q L P A F L E E L	27	-22.64
	257	K L V L D V A H V	27	-20.1
	158	F M N K F I Y E I	26	-20.37
	172	F L Y A P T I L L	25	-19.87
	410	A L A K R S C G L	25	-24.57
	218	L L N Q H A C A V	24	-22.45
	242	K L S Q K F T K V	24	-22.29
	571	V I A D F S G L L	23	-22.76
	599	L I S K T R A A L	23	-23.93
	8	F L I F L L N F T	22	-22.78

A: the epitopes were reported; A: the prediction epitopes whose polynomial scores were less than -24.