Fig. 3

Functional annotation and PPI analysis of the DEGs in the wild-type T1 strain. a The number of differentially expressed genes are shown by functional categories, where circle sizes are proportional to the number of genes with significant differential expression. Green circles represent genes with increased expression and red circles represent genes with diminished expression. Only terms with > 2 genes assigned to a functional category are shown. b PPI analyses were carried out using the STRING database analysis tool and line thickness indicates the strength of data support for each interaction. Only connected nodes and interaction with a medium (> 0.4), high (> 0.7) and highest confidence (> 0.9) are visualized in the network. Node colors represent enriched functional categories and gene identification color represents up-regulation (green), down-regulation (red) and unchanged expression (gray). p-value of PPI interactions indicates significance of protein association. a The STRING PPI network of the T1 strain contained 75 nodes and 298 edges with PPI interaction enrichment p-value of < 1.0e-16 (Additional file 5: Figure S4). 4 enriched categories are shown: TCA cycle (green), oxidative phosphorylation (red), ribosome (blue) and HtaA domain (pink). c Enrichment analysis was conducted using STRING and significant expressed categories (FDR < 0.01) are indicated