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Figure 1 | BMC Genomics

Figure 1

From: Gene Set Enrichment Analysis (GSEA) of Toxoplasma gondii expression datasets links cell cycle progression and the bradyzoite developmental program

Figure 1

Alkaline stress is associated with perturbation of cell cycle gene expression. A: Cell Cycle Gene Set Sizes. Sizes of gene sets plotted against time of peak expression. Genes identified as S/M or G1 stage genes differentially expressed within the cell cycle [14] were assigned to gene sets that reflected genes expressed at different time points in the cell cycle. Assignments were made regardless of peak expression time, so that genes could belong to more than one gene set. Blue dots are G1 gene sets and green crosses indicate S/M gene sets. The red line indicates minimum size of gene set (15 genes) to be used with GSEA. Blue and green bars at bottom indicate phases of an eight hour RH strain tachyzoite cell cycle [14]. B: Cell Cycle Gene Expression of Tachyzoites and in vitro Bradyzoites. Gene expression arrays from tachyzoites and in vitro bradyzoites previously reported [11] were analyzed by GSEA. The plot shows normalized enrichment scores (NES) obtained from GSEA for those cell cycle gene sets with significant enrichment (FWER-adjusted p < 0.05) after GSEA analysis. A positive NES indicates that the gene set is associated with unstressed, tachyzoite parasites, while a negative NES indicates that the gene set is associated with alkaline stressed, in vitro bradyzoites. C: RHΔgcn5A mutant cell cycle gene expression. Transcriptomes of alkaline stressed Δgcn5A parasites and alkaline stressed wild-type tachyzoite [12] were compared by GSEA. Plotted normalized enrichment scores (NES) for those cell cycle gene sets with significant enrichment (FWER-adjusted p < 0.05). A positive NES indicates that the gene set is associated with RHΔgcn5A mutant parasites lacking GCN5A; negative NES indicates that the gene set is enriched in the transcriptome of alkaline stressed parental wild-type RH parasites.

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