There were only five association rules that involved epitopes from the Env gene. Four of these five were from Gag-Env

and one from Pol-Env associations. Notably, associations with antibody epitopes were limited to these five Env association rules, which can partially be attributed to the high degree of sequence divergence among the Env FK228 mouse sequences that can differ by as much as 30% I-BET151 at the amino acid level [76]. Figure 2 Relative composition of unique association rules involving multiple genes ( Gag , Pol and Nef ) and epitope types (Cytotoxic T Lymphocyte (CTL), T-Helper (Th) and antibody (Ab) epitopes). The 6142 unique association rules are classified according to the genes that harbor these epitopes. The pie-chart inside each segment represents the division according to the epitope region types involved. The single association rule in Nef-only category involved CTL and Th epitopes, while that in Pol-Env category involved CTL and Ab epitopes. Out of four association rules involving epitopes from Gag and Env, three belonged to CTL-Ab and one belonged to Th-Ab epitope regions types. No association rules included all three types of epitopes (CTL, Th and Ab) and

four genes (Gag, Pol, Env and Nef). MAPK inhibitor However, several “”multi-type”" association rules comprised of two different epitope types (CTL and Th) and three genes (Gag, Pol and Nef) were discovered (Figure 1, Additional file 5). For example, in the association rule: GHQAAMQML (CTL, Gag) – PKEPFRDYV (Th, Gag) – KLNWASQIY (CTL, Pol) – FLKEKGGL (CTL, Nef) (Figure 1), GHQAAMQML, KLNWASQIY and FLKEKGGL are CTL epitopes from the Gag, Pol and Nef genes, respectively, while PKEPFRDYV is a Th epitope from the Gag gene. Overall, there were 137 “”multi-type”" associations involving

epitopes from two types and three genes (2T-3G) among a total of 21 CTL and Th epitopes from the Gag, Pol and Nef genes (Additional Abiraterone file 5). These 21 epitopes can be mapped to 14 different non-overlapping genomic regions (Table 3) and a single association rule is generally spread across 3 to 5 of such regions. Interestingly, even though the association rule with the maximum number of epitopes in a single rule (9 epitopes) involved four non-overlapping genomic regions, it included epitopes from only two genes, Gag and Pol. Epitope-associations in the reference genome are representative of the global HIV-1 population Presence of association rules discovered in the reference genome set was verified by analyzing a larger worldwide set of 978 HIV-1 genomes (including 888 sequences from the 2008 web alignment and 90 reference sequences from the HIV Sequence database). The Gag, Pol and Nef genes in each sequence were concatenated for the purpose of the analysis, and presence of each association rule (as a complete match of all epitope regions involved) was noted. The results showed that most of the epitope-associations were present in the majority of genomes from the global HIV-1 population.