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Fig. 4 | BMC Genomics

Fig. 4

From: Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

Fig. 4

Hypergeometric 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 HATS

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