Fig. 5
Genes with significant expression fold changes organized by categories for pairwise comparisons of the transcriptomes in the pfcrt 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 the 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. To identify significant differences, we applied a threshold of a fold change >1.5 and a normalized fold change at least 2 standard deviations (SD) above the mean for higher gene expression, and a threshold of a Fold change <0.6 and a normalized fold change 3 SD below the mean for lower expression. a Genes with higher expression in the parental line 7G8 in comparison to the recombinant control strain 7G8pfcrt_CTL. b Genes showing higher expression in 7G8 compared to the recombinant back-mutant strain 7G8pfcrt_T76K. c Venn diagrams depicting the overlap of genes with higher (fold change >1.5, left) or lower (fold change <0.6, right) expression in 7G8 for both 7G8 vs. 7G8pfcrt_CTL and 7G8 vs. 7G8pfcrt_T76K pairwise comparisons. d Genes with lower expression in comparison with the recombinant control strain 7G8pfcrt_CTL. e Genes with lower expression in the parental line 7G8 in comparison with the recombinant back-mutant strain 7G8pfcrt_T76K