Discovery of novel targets for multi-epitope vaccines: Screening of HIV-1 genomes using association rule mining

Retrovirology

Table 4 Properties of 22 CTL epitopes that frequently co-occur together in the reference HIV-1 genomes (per the 62-all sequence set).

Gene	Protein	Non overlapping genomic regions	Amino acid sequence	HLA allele *	Amino acid Coordinates		Number of "unique" association rules each epitope is involved	Number of association rules each region is involved
					Start	End
Gag	p24	1	SPRTLNAWV	B*0702	16	24	2	2
		2	SEGATPQDL^#	B*4001	44	52	127	72
		3	GHQAAMQML^#	B1510, B3901	61	69	214	110
		4	KRWIILGLNK^##	B*2705	131	140	7	95
			GLNKIVRMY	B*1501	137	145	195
			VRMYSPVSI	Cw18	142	150	1
Pol	RT	5	IETVPVKL	B*4001	5	12	9	9
		6	KLVDFRELNK	A*0301	73	82	188	100
		7	GIPHPAGLK	A*0301	93	101	124	73
		8	TVLDVGDAY^###	B*3501	107	115	38	31
		9	NETPGIRYQY	B18	137	146	14	9
			IRYQYNVL	B*1401	142	149	11
		10	LVGKLNWASQIY	B*1501	260	271	112	51
			KLNWASQIY	A*3002	263	271	114
	RT-RNase	11	IVTDSQYAL	Cw*0802	495	503	149	69
			VTDSQYALGI	B*1503	496	505	153
	RT-Integrase	12	LFLDGIDKA	B81	560	8	121	68
	Integrase	13	KTAVQMAVF	B*5701	173	181	52	39
			AVFIHNFKRK	A0301, A1101	179	188	15
			FKRKGGIGGY	B*1503	185	194	4
		14	VPRRKAKII	B42	260	268	2	2
Nef		15	FLKEKGGL^###	B*0801	90	97	52	34

These epitopes are harbored by 15 different protein-coding genomic regions. For each epitope and genomic region the number of "unique" association rules (as defined in Table 2) is shown, as well as the corresponding HLA alleles that recognize that particular CTL epitope.
* HLA alleles as defined in the HIV Molecular Immunology Database, Los Alamos National Laboratory.
^#, ^## and ^### designate potentially promiscuous CTL epitopes that are: (^#) recognized by alternative HLA alleles, (^##) potentially embedded, or (^###) shared between allele pairs (per [59]).

ISSN: 1742-4690