PMC

Relationship between tachyzoite cDNA/reference ratios and tachyzoite EST frequency in the ME49 tachyzoite library. The dashed line represents the median tachyzoite cDNA/reference ratio for all contigs on the microarray. Bars represent the mean tachyzoite cDNA/reference ratio for the contigs in each class. Ratio values for each class are significantly different from each other (P < 0.0001 [unpaired Kruskal-Wallis test]).

Bradyzoite/tachyzoite signal intensity ratios as measured by a type I experiment versus a type II experiment. The log₂ ratio for 3,644 quality spots from both experiments is shown. The box in the upper right quadrant indicates spots that are considered induced (ratio ≥ 1.95) in both experiments, and the box in the lower left quadrant indicates spots that are considered repressed (ratio ≤ 0.66) in both experiments.

Clustering of genes based on transcript abundance in bradyzoites. Genes within the “induced” classes shown in Fig. are clustered based on the bradyzoite cDNA/reference ratio. The median signal intensity ratios for each of the three time points were essentially equal to 1.0 (1.04 for day 2, 1.03 for day 3, and 0.99 for day 4), allowing the relative abundance for all three time points to be represented on the same scale, as described for Fig. . The number given for each gene is the Ctoxoqual contig number.

Northern blot analysis of developmentally regulated genes identified by microarray experiments. The signal for each gene in day 2 tachyzoites and day 4 bradyzoites is shown. The fold change values calculated by each method, Northern blot and microarray, are given to the right of the blots for each gene. No fold change value could be calculated for SRS9 or Ctoxoqual_2199 based on Northern blots due to the absence of signal in either the tachyzoite or bradyzoite sample. Each image shows the results from repeated probing of the same blot. In each case only a single band per lane was detected.

Distinct classes of developmentally regulated genes and tachyzoite transcript abundance levels. The tachyzoite cDNA/reference ratios are shown in the left column, represented on a scale of gray (below the median value for all contigs) to white (equal to the median value for all contigs) to blue (above the median value for all contigs). The mean bradyzoite/tachyzoite ratios for all time points are shown in the columns to the right, represented on a scale from green (induced) to red (repressed). Genes represented by singleton ESTs are not included in this cluster. Fold change values that were not statistically significant according to SAM are marked with an asterisk and were not used in clustering the genes into distinct classes. Classes are based on the bradyzoite/tachyzoite expression patterns. The number given for each gene is the Ctoxoqual contig number. Locations or functions (either known or predicted) of genes are given in parentheses. Gene abbreviations: SAG, surface antigen; PPD, pyridoxal phosphate dependent; LDH, lactate dehydrogenase; SRS, SAG1-related sequence; MAP, methionine aminopeptidase; BAG, bradyzoite antigen; ENO, enolase; DRPA, homologue of deoxyribose phosphate aldolase; MIC, microneme; ROP, rhoptry; G6PD, glucose-6-phosphate dehydrogenase; GRA, dense granule; NTPase, nucleoside triphosphate hydrolase.