Frequent associations between CTL and T-Helper epitopes in HIV-1 genomes and implications for multi-epitope vaccine designs

Table 2 Overview of epitopes used in the analyses.

Gene	Protein	Total no. of epitopes				Highly conserved epitopes*				No of associated epitopes^{^}
		CTL^#	Th	Ab	Total	CTL	Th	Ab	Total	CTL	Th	Ab	Total
Gag	p17	18	32	-	50	1	-	-	1	-	-	-	-
	p24	42	88	1	131	8	6	-	14	8	6	-	14
	p2p7p1p6	6	18	-	24	2	-	-	2	2	-	-	2
	Total	66	138	1	205	11	6	-	17	10	6	0	16
Pol	Gag-Pol	1	-	-	1	-	-	-	-	-	-	-	-
	Protease	8	-	-	8	1	-	-	1	1	-	-	1
	RT	39	20	3	62	12	1	-	13	12	1	-	13
	RT-
	Integrase	1	1	-	2	1	-	-	1	1	-	-	1
	Integrase	12	11	-	23	5	2	-	7	4	2	-	6
	Total	61	32	3	96	19	3		22	18	3	0	21
Vif		9	2	-	11	-	-	-	-	-	-	-	-
Vpr		7	6	-	13	-	-	-	-	-	-	-	-
Tat		4	6	1	11	-	-	-	-	-	-	-	-
Rev		4	5	-	9	-	-	-	-	-	-	-	-
Vpu		1	1	-	2	-	-	-	-	-	-	-	-
Env		40	82	75	197	-	-	2	2	-	-	1	1
Nef		37	24	1	62	2	1	-	3	2	1	-	3
	Total	229	296	81	606	32	10	2	44	30	10	1	41

^# CTL epitopes included only the best-defined epitopes as described by Frahm et al. (2007) [56]
* Only those epitopes present in more than 75% of the reference sequences were considered as highly conserved and thus included in the association rule mining. 3 epitopes completely overlapping with other epitopes of same type without amino acid differences were not included.
^{^} Associated epitopes are epitopes involved in association rules identified with a support value of 0.75 and confidence value of 0.95

ISSN: 1471-2180