Nucleic Acids Research, 2006, Vol. 34, No. 4 1171 Figure 3. Multiple var genes are expressed during the IDC. The gene expression profiles of all var genes measured for the 3D7 strain along with the respective profiles from Dd2 and HB3 are displayed. The genes are organized according to var gene group as defined by Lavstsen et al. (30). in this region suggests that HB3 may utilize different surface proteins during merozoite invasion. To determine whether transcripts with high AVG SOM values actually represent the most abundant gene products within the cell, we compared the most abundant transcripts in our study to the most highly identiﬁed proteins in two proteomics studies performed on selected stages of the IDC (25,26). Of the 100 most abundant proteins detected by mass spectrometry (as determined by peptide count in red blood cells stages), 50% are in the 200 most abundant transcripts by our microarray analysis, while 75% are in the top 500 transcripts. Le Roch et al. also reported a concordance between mRNA transcription and protein expression and noted a timing lag between these two processes (27). This demonstrates that there is a strong correlation between tran- scription levels and translation for P.falciparum. Putative deleted, polymorphic and silenced regions Based on our transcriptome analysis, we identiﬁed several compelling chromosomal regions for further characterization. On chromosome 4 a 20 kb region containing two proteins with homology to reticulocyte binding proteins (PFD1150c and PFD1155w) and a hypothetical gene (PFD1160w) is not expressed and may be silenced in HB3 and Dd2, but contains several genes that are expressed during the 3D7 IDC. This is not due to a chromosomal deletion, since these regions are present by CGH analysis (E.D.W. and J.L.D., personal com- munication). Furthermore, PFD1150c (PfRh4) has recently been demonstrated to be required for switching from sialic acid dependent to independent modes of invasion (28). Thus, the observed difference in gene expression suggests that tran- scriptional regulation varies at this locus between strains and is important for invasion. Another chromosomal region with large detectable differences in gene expression is the ﬁrst 100 kb of chromosome 2, a region known to be polymorphic and associated with cytoadherence (23). In this region, we solely detected gene expression for four riﬁn genes, a highly expressed PfEMP3, several hypothetical genes, and a PfEMP1 gene in the 3D7 strain. Immune evasion: var, stevor, rifin genes P.falciparum modulates host immune response by switching on a vast repertoire of surface proteins in successive parasite generations (29). The three major families of variant surface proteins are the var genes (PfEMP1 proteins), the repetitive interspersed gene family (riﬁns) and the subtelomeric variant ORFs (stevors). Our microarray contains probes for 50 of the 59 vars, 28 of the 29 stevors and 141 of the 154 predicted riﬁns. It is well established that P.falciparum expresses only a subset of var genes per IDC, which are replaced by other var genes in later generations (29). In our analysis of the 3D7 strain we detected 16 var genes. Overall, the maximal expres- sion of these genes occurred during the late ring and early trophozoite stages and was synchronized with expression of KAHRP and PfEMP3, the structural elements of knob protru- sions (Figure 3), with the exception of PF08_0142, which intriguingly showed maximal expression at the late trophozoite-early schizont-stage. These transcripts represent each of the ﬁve major groups of var genes, suggesting that at least one member of each category is expressed per IDC (30). In a prior 3D7 transcriptome study, a completely differ- ent set of var genes was detected indicating that even lab- adapted strains utilize different cohorts of these genes (31). We detect little to no expression for any stevor genes which supports evidence for a role in cytoadhesion in the gametocyte developmental stage (32). We measured gene expression for a small subset of riﬁns which peaks between 15–17 h post- invasion, supporting their previously reported role in adhesion (33). Therefore, even in vitro different sets of P.falciparum surface proteins are being expressed. DISCUSSION The malaria parasite P.falciparum has evolved and adapted to locations worldwide where the Anopheles mosquito survives and co-exists with humans, resulting in a wide range of inter- strain differences in virulence and drug resistance. Unfortu- nately, the basis for strain-speciﬁc phenotypic variability in P.falciparum remains poorly characterized with the exception