Hundreds of genes differentially expressed between strains including potential AP2 regulators.

A) Using edgeR, we identify genes that are differentially expressed between strains (FDR <10%), generating three gene lists for tachyzoite condition and three for the bradyzoite condition. We generated Venn diagrams showing the overlap between the lists in the tachyzoite condition and bradyzoite condition. We also compared tachyzoite and bradyzoite gene lists to each other. Venn diagrams shows comparison of genes that appear in both the tachyzoite and the bradyzoite lists and therefore are “stage independent”. AP2 containing genes appearing on more than one list (any intersection) are indicated. The complete set of genes that are differentially expressed are listed in Table S2 and RPKM values for all replicates are listed in Table S1. B) Heat map of genes differentially expressed following CTG bradyzoite differentiation in all six conditions. Red indicates up regulation compared to that gene's expression level under other conditions, whereas green indicates down regulation. Conditions (columns) are clustered based on similarity of expression levels. The five AP2 genes that are differentially expressed are indicated on the right. Heat map was generated using the 'heatmap.2' function in the 'gplots' package for R. Hierarchical clustering of both the rows (genes) and columns (conditions) computed by the 'hclust' function in the R 'stats' package. Based on mean of replicate RPKM values.