Fig. 2

Comparison of the K. pneumoniae CH1034 gene expression levels across the different conditions. a The expression levels of the 5 146 CDS and the 44 ncRNA genes of the K. pneumoniae CH1034 genome were compared in each of the 10 possible pairs of conditions. The number of differentially expressed (∣fold-change∣ > 5 and adjusted P-value < 0.01) CDS and the number of ncRNA genes, shown in parentheses, are indicated for each comparison. b Principal component analysis (PCA) of gene expression in the five growth conditions. PCA was performed with Z-score values of the 2 052 CDS and 19 ncRNA genes differentially expressed (∣fold-change∣ > 5 and adjusted P-value < 0.01) in at least one of the 10 possible pairs of conditions. Z-score values were calculated with absolute expression values normalized by the DESeq package, and were used as a matrix to perform a PCA with package FactoMineR of R/Bioconductor. Each dot indicates a biological replicate. The lists of these 2 052 CDS and the 19 ncRNA genes are provided respectively in Additional file 2: Table S1 and Additional file 3: Table S2