Fig. 4

Overall trends in whole blood gene expression analysis of P. knowlesi infected pig-tailed macaques. A Volcano plot for first baseline versus second baseline. All volcano plots based on a False Discovery Rate (FDR) < 0.2, with upregulated genes shown in red and downregulated genes in blue. The number of Differentially Expressed Genes (DEGs) are indicated in each plot. B Gene Set Enrichment Analysis (GSEA) for blood transcription modules enriched in first baseline versus second baseline. GSEA based on an FDR of 0.05. NES, normalized enrichment score. C UpSet plot showing total DEGs for each infection timepoint versus the relevant baseline, and shared DEGs between infection timepoints. D–G Volcano plot for each infection timepoint versus the relevant baseline. All samples from cohort 2 animals