File:Three-way differential expression (DE) plot shows three distinct states in the T. gondii wild-type asexual cycle.tif

English: This plot slices the 8058 predicted T. gondii genes, (each point represents a gene) into specific gene sets that reflect all possible comparisons of intracellular tachyzoites (IT), extracellular tachyzoites (ET) and bradyzoites after 72 hr induction (B72); (IT – ET, B72 – ET, and B72 – IT). Each comparison is associated with a dashed axis, which captures the magnitude of differential expression associated with the comparison, and two solid lines, which bound the set of genes differentially expressed less than 2-fold by the comparison. Of the 8,058 probe sets, 6,096 (central hexagon) are not changed more than 2-fold between any of the 3 states. The extracellular tachyzoite-specific genes lie at the intersection between genes that are up-regulated in extracellular tachyzoites compared to intracellular tachyzoites (IT-ET ≤−1; n = 419, below the green solid line) and genes that are upregulated in extracellular tachyzoites compared to bradyzoites (B72-ET ≤−1; n = 447, to the left of the red solid line), which total 122 genes. The intracellular tachyzoite-specific genes lie at the intersection between genes that are up-regulated in intracellular tachyzoites compared to extracellular tachyzoites (IT-ET ≥1; n = 609, above the green solid line) and genes that are up-regulated in intracellular tachyzoites compared to bradyzoites (B72-IT ≤−1; n = 308, above the blue solid line), which total 149 genes. And, the bradyzoite-specific genes lie at the intersection between genes that are up-regulated in bradyzoites compared to extracellular tachyzoites (B72-ET≥1; n = 738, to the right of the red solid line) and genes that are up-regulated in bradyzoites compared to intracellular tachyzoites (B72-IT≥1; n = 604, below the blue solid line), which total 418 genes.