Nucleic Acids Research, 2006, Vol. 34, No. 4 1169 Figure 1. IDC Transcriptomes for three P.falciparum strains. The phaseograms depict the 48 h progression of gene expression throughout the IDC from the early ring-stage to merozoite invasion (left to right) for the 3D7, Dd2 and HB3 strains of P.falciparum. The profiles have been ordered (top to bottom) by the phase of gene expression during the IDC and demonstrate a highly similar cascade across the three strains. Depicted above the phaseograms (in gray scale) is the relative percentage of the three morphological stages: ring, trophozoite (troph) and schizont. Table 1. Total number of shared and unique oligo probes measured in the three strains, with the percent of the total number of measured probes for each strain Oligo group Total measured probes All three strains HB3 and 3D7 only Dd2 and HB3 only Dd2 and 3D7 only HB3 only 3D7 only Dd2 only 5193 739 35 62 448 296 4 3D7 6287 82.5% 11.8% — 1.0% — 4.7% — Dd2 5294 98.1% — <1.0% 1.2% — — <1.0% HB3 6415 81.0% 11.5% <1.0% — 7.0% — — these phase differences result from spurious FFT phase cal- culations due to noisy gene expression proﬁles that derive from low intensity data and may not reﬂect true differences. Overall, the majority of proﬁles are very similar by phase and do not suggest widespread variations in gene expression between strains. The expression proﬁles of the HB3 and Dd2 strains demonstrate the least difference in phase, while HB3 and 3D7 are the most distant. Since the FFT calculation is most useful for comparing high amplitude gene expression proﬁles, an alternative approach was necessary to gauge proﬁle similarity for all genes. We chose to use the Pearson correlation, since this measure is insensitive to overall amplitude differences. We calculated Figure 2. Inter-strain differences in gene expression are rare during the IDC. The differences in gene expression profiles as measured by Pearson correlation and the FFT phase are low between all strains measured here. (A) Depicts the distribution of the Pearson correlation between gene expression profiles from the 3D7 and HB3 datasets. 70% of the correlations are greater than 0.7. The inset plots the nearly linear relationship for most of the FFT phases for these two strains. The largest differences in phase are within the red circles. The arrows point to a gene with a significant change in phase between 3D7 and HB3 (MAL13P1.344) and another gene with virtually no difference (PFI1740c). The Pearson correlation and phase change between 3D7 and HB3 for these two genes are shown with the expression profiles from all three strains (B). Northern blot of MAL13P1.344 (C) shows mRNA transcript levels at the ring (R) and schizont (S) stages of development for the 3D7, Dd2 and HB3 strains of P.falciparum. Transcription of this gene in HB3 is out of phase with that measured in 3D7 and Dd2. the correlation for all pairwise probe to probe comparisons between strains (see Materials and Methods) (Supplementary Table S9). The Pearson correlation for more than 70% of measured proﬁles is greater than 0.7. These high correlations demonstrate an excellent agreement in gene expression between strains and indicate a strong preservation of the over- all timing of transcriptional regulation throughout the IDC (Figure 2A and B).