Figure 3

Classification of differentially expressed genes across the whole IDC and validation of differential expression of 5 genes by qPCR. (a) Plot of the Ranked Product Score for all 4,015 genes calculated from the geometric mean of the ranked z-scores of the genes in the 3 stages in the generated transcriptome (orange) and in the randomized dataset (green) (for details see material and methods). The graphs represent 4 over (b) and 4 under-expressed (c) genes in the resistant parasites with potential regulatory functions present in the top 5% of each extreme of the rank product distribution, respectively ((a) grey boxes). Data points represent the mean log₂ expression ratios of the genes in the resistant (green triangle), susceptible Lao and Thai (blue diamond), and susceptible Cambodian isolates (CP022, purple circle) across the three selected stage intervals. The data are projected onto the gene expression profiles analyzed by the in vitro IDC transcriptome (red square). Error bars reflect the standard deviation of the log₂ ratios for each data point. (d) Bars represent the log₂-transformed fold change measured from relative quantification of a resistant versus a sensitive isolate using PFC0965w as a reference control gene in real-time PCR experiments (teal) and plotted alongside the microarray expression ratios (light blue). Error bars reflect the standard deviation of the log₂ ratios over triplicates.