Additional file 11: Table S6 of Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1

Genes (A-D) and gene sets (E-H) differentially expressed in the pfmdr1 data set. For each pairwise comparison, we listed genes with significant differential expression, i.e. with a fold change greater than 1.5 and a normalized fold change two standard deviations above the median values and genes with a fold change lower than 0.6 and a normalized fold change three standard deviations below the median value, which generally represented the quasi-totality of genes with a fold change below 0.6. Normalization was performed using the average fold change computed across a background pool of 11 transcriptome data sets as a scaling factor. This normalization allowed us to identify and filter out most of the hypervariable genes (e.g. var, rifin, stevor, phist, and hyp). Antigenically variant genes not detected by automatic filtering were manually removed. We listed the gene sets with significant differential expression (based on the mean rank of enrichment score >0.9 (significantly enriched) or <0.1 (significantly impoverished)) that are found in both FCB vs. FCB pfmdr1_3′KD and FCB vs. 106/1 pairwise comparisons. (XLSX 65 kb)