Differential expression between clonal lineages. A , MA plots (intensity ratio versus average intensity) for hybridizations with representatives of the three major clonal lineages of Toxoplasma show a very high degree of reproducibility among biological replicates (comparisons shown along diagonal), and a significant number of differentially expressed genes between lineages (blue dots). Tables list genes exhibiting the greatest differences in hybridization intensity for each pairwise comparison, ranked by estimated fold-change (asterisks indicate genes where at least four probes are polymorphic). B , Gene presence was determined using a 10% false discovery rate (see Materials & Methods for details), resulting in 42% of genes called present in RH-, 38% in Prugniaud-, and 40% in VEG-strain parasites, with an aggregate total of 49% of genes called present in any strain during the tachyzoite (lytic) life stage. C , 5,307 genes exhibit differences in between-strain expression levels at a P-value of 1 × 10-3 (corrected for multiple testing); filtering to eliminate genes for which 4 or more probes are polymorphic, differences in fold change are under 2-fold, or are called absent (at a 10% FDR) leaves 2,078 genes with clear evidence of strain-specific differential expression. The pie chart indicates the distribution of differentially regulated genes by strain (+ and - indicate up- and down-regulation, respectively).