Figure 3

Identification of patterns of bradyzoite associated gene expression. A: Gene sets associated with tachyzoite-bradyzoite transition. Eight gene sets were derived from the microarray analysis encompassing gene sets with differential expression during the tachyzoite and bradyzoite stages [9]: Genes up-regulated in either 1) in vitro tachyzoites or 2) in vitro bradyzoites were each placed into their own gene sets. Genes up-regulated in either 3) in vitro tachyzoites or 4) mouse-derived bradyzoites were each placed in their own gene sets. Genes up-regulated in either 5) in vitro day 4 bradyzoites or 6) in vitro day 8 bradyzoites were each placed in their own gene sets. Genes up-regulated in either 7) in vitro bradyzoites or 8) mouse-derived bradyzoites were each placed in their own gene sets. Colored lines under each picture correspond to the color coding of enriched gene sets in Panels B and C. B: The transcriptome of alkaline stressed RH parasites is enriched for bradyzoite gene sets. Transcriptomes of wild-type RHΔuprtΔhxgprt tachyzoites and alkaline stressed RHΔuprtΔhxgprt parasites [11] were compared. GSEA-derived normalized enrichment scores (NES) for bradyzoite gene sets are shown. A positive NES indicates that the gene set is associated with unstressed, tachyzoite parasites, negative NES indicates that the gene set is associated with alkaline stressed, in vitro bradyzoites. Color coding of enriched gene sets is identical to that shown in Figure 3A. Stars indicate significant enrichment (FWER-adjusted p < 0.05). C: The transcriptome of RHΔgcn5A parasites is enriched for tachyzoite gene sets under alkaline stress. Plotted normalized enrichment scores (NES) for bradyzoite gene sets. A positive NES indicates that the gene set is associated with Δgcn5A mutant RH parasites missing the GCN5A enzyme [12], while negative NES indicates that the gene set is associated with the parental wild-type RH. Stars indicate significant enrichment (FWER-adjusted p < 0.05).