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. 2022 Nov 15;18(11):e1010968. doi: 10.1371/journal.ppat.1010968

Fig 1. Study design and differential gene expression analysis.

Fig 1

(A) Reinfection study design. (B) Principal component analysis (PCA) of the top 500 genes expressed in the reinfection group. As described in Materials and Methods, patient-specific gene expression variation was removed using the function removeBatchEffect. Time points and groups are indicated by different colors and shapes, respectively. The ellipses denote the core area with a confidence interval of 68% for each group. (C) Number of differentially expressed genes (DEGs) across all reinfection time points. Pre-reinfection time-points were used as a baseline. Genes differentially expressed are selected using a Benjamin-Hochberg adjusted P value < 0.10. (D) Vaccine study design. Vaccine data were obtained from Hartnell et al. [18]. (E) PCA of the top 500 genes expressed in the vaccine group. (F) Number of DEGs across all vaccine samples. d0 and d56 were used as a baseline for prime and boost vaccine time points, respectively. Genes differentially expressed are selected using a Benjamin-Hochberg adjusted P value < 0.05.