Fig. 3

Gene expression changes in cells grown on respiratory relative to fermentative media. a Overlap of protein-coding genes identified by RNA-seq as significant and two-fold differentially expressed and respiratory-deficient mutants of clusters A and P. b Venn diagram of genes identified by RNA-seq as two-fold differentially expressed and previously defined CESR genes [35, 36]. c Fold changes of gene expression on glycerol relative to glucose are plotted against read numbers for transcripts in both conditions. Averages from two independent biological repeats are shown. Stress- and growth-related core environmental stress response (CESR) genes are highlighted in red and blue, respectively. d Fold-change distribution of selected GO categories overrepresented among the differentially expressed genes on glycerol relative to glucose. The widths of boxes are proportional to the number of genes in each category (n). Data obtained using AmiGO web tool (Additional file 1: Table S2). e Top axes: fold changes of gene expression on glycerol relative to glucose plotted along chromosomal gene positions, genes with log2 fold change higher than 3 or lower than −3 are shown in red. Lower axes: chromosomal clusters of co-regulated genes; regions with six or more genes in ten-gene windows along chromosomes being induced or repressed more than twofold are shown in red