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1.
FIG. 3.

FIG. 3. From: HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: Immune Escape and Viral Load .

A comparison of the types of validation support for the individual associations found in the original data set (light-gray bars) and in the extended data set (black bars) that included additional sequences from Gag, Pol, Env, and Nef.

Christine M. Rousseau, et al. J Virol. 2008 July;82(13):6434-6446.
2.
FIG. 2.

FIG. 2. From: HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: Immune Escape and Viral Load .

Immunological map comparing HLA-amino acid associations from subtypes B and C that were within the same epitopes. The light-yellow boxes are the subtype B sequences from a Canadian study (12), and the light-green boxes are the subtype C sequences from this study. The underlined residues represent a site with opposing selective pressures. In this case, it is mediated by the same HLA allele but is in the context of different amino acids three sites upstream.

Christine M. Rousseau, et al. J Virol. 2008 July;82(13):6434-6446.
3.
FIG. 1.

FIG. 1. From: HLA Class I-Driven Evolution of Human Immunodeficiency Virus Type 1 Subtype C Proteome: Immune Escape and Viral Load .

Epitope map of p17 and p24 of Gag showing individual associations and immunological sets. The reference sequence was the consensus of the full-length HIV-1 sequences from South Africa. All significant individual associations identified are shown below the consensus sequence. Blue amino acids reflect the susceptible form and red the resistant form. Shaded boxes indicate immunological sets. The size of the immunological set was determined by both the individual associations and validation data. These sets were chosen to minimize the number of epitopes that explained the observed data, taking linkage disequilibrium and 9-mer overlap into account. Only significant 9-mer regions with two or more associations are shown. For example, if a susceptible and a resistant residue were at a single site, both are shown, or if more than one site was involved in the variation that makes the 9-mer association distinctive, it is shown. If there were conserved amino acids between the HLA-associated variant sites within the 9-mer, they are indicated by small gray letters. When linked HLAs were associated with the same site, the HLA with the lowest P value is shown. An HLA in green indicates that there was a gamma interferon ELISPOT reactivity pattern associated with that HLA that overlapped the associated amino acid change. In the validation area (above the consensus sequence), fuchsia shading over the HLA label indicates motifs, orange indicates B list epitopes, red indicates A list epitopes, and blue indicates predicted epitopes. Similar to the individual associations, epitopes and motifs that were inferred to be susceptible or resistant are also labeled with blue or red letters, respectively. In the association area (below the consensus sequence), a gray background indicates that the association came from linkage disequilibrium. Associations in sites with >90% gaps are not shown. See http://www.hiv.lanl.gov/content/immunology/hlatem/index.html for maps of remaining HIV-1 proteins and the extended data set.

Christine M. Rousseau, et al. J Virol. 2008 July;82(13):6434-6446.

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