Fig. 4From: Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1Hypergeometric Analysis of Time Series (HATS) for pairwise comparisons of the transcriptomes in the pfmdr1 data set. HATS was performed by combining FFT to align the time series with a hypergeometric distribution approach based on random permutations to compute an enrichment score for each gene set. Normalization of the enrichment scores was performed using an expression baseline constituted by a background pool of 11 transcriptome data sets (see Methods). We applied a threshold of normalized gene set rank >0.9 for gene sets we considered positively enriched and normalized gene set rank <0.1 for gene sets considered negatively enriched. Gene sets were built using GO, KEGG and the Malaria Parasite Metabolic Pathway (listed in Additional file 26: Table S17). a Gene sets that are enriched in FCB in comparison to FCBpfmdr1_3′KD (mean ranking values >0.9). b Gene sets that are enriched in FCB in comparison to 106/1 (mean ranking values >0.9). c Gene sets that are depleted in FCB in comparison to FCBpfmdr1_3′KD (mean ranking values <0.1). d Gene sets that are depleted in FCB in comparison to 106/1 (mean ranking values <0.1). e Stage-associated enrichment analysis in FCB in comparison to FCBpfmdr1_3′KD. Gene sets with significant enrichment (orange) or depletion (blue) for three windows of the parasite IDC correspond to rings (R, 12–16 h post-invasion), trophozoites (T, 24–28 h post-invasion) and schizonts (S, 32–36 h post-invasion). f Stage-associated enrichment analysis in FCB in comparison to 106/1. Gene sets with significant enrichment (orange) or depletion (blue) during the same three stages as in (E). g Venn diagrams depicting overlaps of gene sets significantly enriched in FCB (mean rank of enrichment score >0.9) for both FCB vs. FCBpfmdr1_3′KD and FCB vs. 106/1 pairwise comparisons, as identified from our HATS analysis. h Venn diagrams depicting overlaps of gene sets significantly depleted in FCB (mean rank of enrichment score <0.1) for both FCB vs. FCBpfmdr1_3′KD and FCB vs. 106/1 pairwise comparisons, as identified using HATSBack to article page