Fig. 2
Uncorrected differential expression index (DEI) of the ISO-CTR comparison plotted against that of ATE-CTR. Each dot represents one of the 15966 genes for which it was possible to assign DEI values in both treatment groups. The color of the dots reflects the local gene density (the lighter the denser). The DEIs are anti-correlated (r = −0.3). The dashed lines at DEI = ±4.96 for ISO-CTR comparison and DEI = ±7.13 for ATE-CTR correspond to a (corrected) FDR of 0.0001. Genes passing both thresholds are observed in the upper-left and lower-right quadrants only, defining two sets of counter-expressed (CE) genes: CEISO ATE genes (shown in purple) and CEISO ATE (in green); the corresponding gene names are shown in the respective lists (10 genes each). The ordinal number preceding the CE genes reflects the gene rank according to the linear combination of the two DEI indexes. Strain-specific versions of this plot can be found in Additional file 1: Figures S20-S21