Fig. 2

Acute malaria but not malaria relapse causes substantial changes in the bone marrow transcriptome. a Clustered heatmap of the BM transcriptome, with infection points of samples indicated. Four samples from acute primary infection form a cluster separated from other infection points. Another cluster captures more mild infection responses, including four out of six relapse time points. Colours indicate z-score normalized expression values. b Volcano plots of differentially expressed host genes in the BM at acute primary infection, post-peak, and relapse compared to pre-infection. The y axis is the negative logarithm base 10 of the p value. The x axis is the log2 difference in expression values between pre-infection and the infection point of a given plot. The red dotted horizontal line represents FDR = 0.05. Thus, the right arm of dots above the threshold line corresponds to genes significantly upregulated compared to pre-infection; the left arm of dots above the threshold line corresponds to downregulated genes. Red and blue dots for all three plots represent genes upregulated or downregulated (respectively) at acute primary infection, visualizing the fact that few genes differentially expressed at primary infection are differentially expressed during post-peak and relapse, with many genes not even trending in the same direction between the two infection points. c Venn diagram showing the overlap of differentially expressed genes at acute primary infection, post-peak and relapses