Fig. 3
Strain-specificity index (SSI) of the ISO-CTR comparison plotted against that of ATE-CTR. Each dot represents one of the 14537 genes for which it was possible to assign SSI values (i.e. the genes were not filtered out in at least 12 out of the 18 available strains in both the ISO-CTR and the ATE-CTR comparisons). The color of the dots reflects the local gene density (the lighter the denser). The SSIs are slightly correlated with each other (r ≈ 0.007, p ≈ 9.0 × 10−21). The two groups of CE genes, CEISO ATE (in purple) and group CEISO ATE (in green) have relatively low SSIs compared to the bulk of genes and their SSIs are strongly correlated with each other (CEISO ATE: r ≈ 0.76, p ≈ 0.01; CEISO ATE: r ≈ 0.51, p ≈ 0.13). Thus, the expression of genes playing a key role at the transcriptional level appear to be less influenced by the strain (lower SSI than the bulk genes) and the treatment (CE genes fall closer to the diagonal than bulk genes) with respect to the other genes