Figure 4.

KEGG pathway analyses for differentially expressed genes. (A) Significant up- and down-regulated pathways upon hyperosmotic challenge. P-value < 0.05 and FDR < 0.25 were used as a threshold. Log2P is the logarithm of P-value. (B) Gene set enrichment analysis (GSEA) of representative up-regulated KEGG pathways under short-term hyperosmotic stress. The four scoring plots represent galactose metabolism (upper left), fructose and mannose metabolism (upper right), phosphotransferase system (lower left) and pyruvate metabolism (lower right) with FDR of 0.010, 0.054, 0.110, and 0.184 respectively. The upper left section of each plot shows the progression of the running enrichment score and the maximum peak therein. The middle left section shows the genes in the pathways as “hits” against the ranked list of genes. The bottom left section shows the histogram for the ranked list of all genes in the expression data set. The right section of each plot shows the expression intensity of genes mapped into each pathway: red (high expression value), blue (low expression value).

Liu et al. BMC Microbiology 2013 13:275   doi:10.1186/1471-2180-13-275
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