Fig. 3
Genes with significant expression fold changes organized by categories for pairwise comparisons of the transcriptomes in the pfmdr1 data set. Gene expression fold changes were calculated as the difference between the areas under the curve generated on the full 384 time point data and were then normalized using a baseline created by a background pool of 11 transcriptomes. For each gene, all 55 possible pairwise combinations of transcriptomes created a distribution of expression fold changes, which was used as a normalization factor. a Genes showing higher expression in the parental line FCB in comparison to pfmdr1-knock-down strain FCBpfmdr1_3′KD. To identify significant differences in gene expression, we applied a threshold of a fold change >1.5 and a normalized fold change at least 2 standard deviations (SD) above the mean. b Genes showing higher expression in FCB in comparison to 106/1. c Genes showing lower expression in the parental line FCB compared to the knock-down strain FCBpfmdr1_3′KD. We applied a threshold of a fold change <0.6 and a normalized fold change 3 SD below the mean. d Genes showing lower expression in FCB in comparison to 106/1. e Venn diagrams depicting the overlap of genes with higher (fold change >1.5, left) or lower (fold change <0.6, right) expression in FCB for the FCB vs. FCBpfmdr1_3′KD and FCB vs. 106/1 pairwise comparisons