Expression profiles of genes showing interesting differences between the strains. A, B) Clusters containing genes that showed higher relative expression in the D-xylonate producing strain compared to the control strain: A) Clusters NP11, NP13 and NP25 identified in the normalized profiles clustering analysis, and B) corresponding clusters FC11, FC13 and FC14 from the fold-change clustering analysis. C) Clusters NP2 and NP3 from the normalized profile clustering, containing genes with delayed response (at 23 h) in the D-xylonate producing strain. D, E) Clusters containing genes showing relatively lower expression in the D-xylonate producing strain; D) Clusters FC1 and FC3 from the fold change clustering, and E) corresponding clusters NP15 and NP20 from the normalized profile clustering showing the relativity of the apparent down-regulation seen in clusters FC1 and FC3. The numbers of genes shared between NP and FC clusters are listed in Additional file 3.