Figure 4
Identification and functional annotation of TIGK genes significantly dependent on PPAD activity. (A) Scatterplot of log2 fold-change (log2FC) in gene expression of TIGKs infected with P. gingivalis WT vs. control (y-axis), and P. gingivalis PPADC351A vs. P. gingivalis WT (x-axis). Genes altered exclusively in the P. gingivalis WT vs. control comparison are displayed in red when significantly up-regulated (log2FC > 0.5, FDR q < 0.05) and in green when significantly down-regulated (log2FC > 0.5, FDR q < 0.05). Genes showing a significant degree of dependence on PPAD activity (significant up-regulation in the P. gingivalis WT vs. control comparison, and significant down-regulation in the P. gingivalis PPADC351A vs. P. gingivalis WT comparison) are highlighted in blue. (B) Clustered heatmap of PPAD-dependent genes. (C) Functional annotation of PPAD-dependent genes in the GS: gene network. The latter connects PPAD-dependent genes (blue font) with key terms (black font) and the associated terms (gray font) identified using ClueGO. Each field of the heat map is color coded to represent the per-row z-score of the gene expression value of the respective gene and sample.
