Fig. 3: Proportion of Mamu-E allele group expression.

a The proportion of Mamu-E expression from G2 (dotted line, n = 6), G2 with promoter LTR (G2_LTR, dashed line, n = 6), and G3 (solid line, n = 20) alleles is shown over the course of the pre-challenge phase for animals expressing alleles from these groups. Alleles from animals later protected from SIV infection are shown as blue lines, while those not protected are shown as red lines. Animals are stratified into quadrants based on their vaccine groups (O, S, X, and E). b, c Average Mamu-E expression from G1 alleles stratified by the allele groups present in animals (G1: n = 18, G2: n = 5, G2_LTR: n = 6, G3: n = 20). The proportion of G1 allele expression is shown in (b), while expression is shown in transcripts per million (TPM) in (c). d For each animal with an allele from the second group of alleles (G2, G2_LTR, or G3), the spearman correlation is computed between G1 and the second group using all pre-challenge time points. e Total Mamu-E expression, where each line represents an animal that is protected (blue, n = 22) or not protected (red, n = 21). The black dashed line indicates the median expression trend. Significance is determined by comparing expression at timepoint with baseline (W0D0). Since no difference was observed between protected and non-protected animals, significance tests were performed with all animals together. In b–d, boxplots are defined by quartiles (upper, median, lower) with whiskers extending to data points up to 1.5 times the interquartile range. In all cases b–c, e Wilcoxon rank-sum tests were used. ****p < 0.001, ***p < 0.01, **p < 0.05, *p < 0.1, ns = not significant.