HIV-1 Immune Escape Maps Figure 4. Integrase Immune Escape Map. doi:10.1371/journal.pone.0006687.g004 covariation corrected) are also differentiated. P- and q-values represent the minimum values observed in the covariation corrected and non-covariation corrected analyses. Found at: doi:10.1371/journal.pone.0006687.s001 (0.23 MB XLS) Table S2 Amino acid-amino acid (aa-aa) associations in HIV-1 Gag, Protease, Reverse Transcriptase, Integrase and Nef (all q,0.2). Consistent with the immune escape maps and supple- mentary table 1, amino acid numbering begins with 1 for each individual protein. Predictor Codon and Target Codon refer to the predictor and target attributes, respectively, however it is important to note that this terminology does not imply a specific direction of association. For example, if one is interested in all codons that covary with Gag codon 242, one should investigate all target codons that appear when 242 is set as the predictor variable, and vice versa. The union of these two searches will provide a list of candidate codons that covary with codon 242. In the case of aa- aa associations, adapted refers to positive associations (ie amino acid pairs that statistically tend to co-exist/co-vary) while nonadapted identifies negative associations (ie amino acids that statistically tend not to be found together). Finally, note that in the original analysis, HIV codon covariation was analyzed across all three Pol proteins simultaneously. However, to maintain consis- tency with Figures 1-5 in the paper, the data listed in this supplementary table are limited to intra-protein associations only, a fact which should be considered when interpreting the q-values for aa-aa associations in Protease, RT and Integrase. Found at: doi:10.1371/journal.pone.0006687.s002 (1.13 MB XLS) Acknowledgments The authors wish to thank Bette Korber and the research team at the Los Alamos National Laboratory for inspiring the original design and layout of the immune escape maps. The authors wish to thank ACTG 5128 and 5142 team members and site staff, HLA and viral sequencing laboratory staff, and patient volunteers in all study sites who contributed to this study. PLoS ONE | www.plosone.org 8 August 2009 | Volume 4 | Issue 8 | e6687