Figure 6: Heatmap showing hierarchical clustering of samples (x-axis) and differentially expressed genes (y-axis) for the control and DEP treatment. Cluster color represents the expression level of genes in log2CPM (Counts per million reads).
The 324 differentially expressed genes in the DEP treatment were annotated to gene ontology (GO) terms, which describe gene properties and group each into one of three categories: Cellular component, molecular function, and biological process. We used GO enrichment analysis to find the most over- and underrepresented term. The 30 most significantly upregulated GO terms in the DEP treatment include protein-binding functions, enzyme complexes and metabolic, especially catabolic, processes (Figure 7A ). The 30 most significantly downregulated GO terms in the DEP treatment include transferase activity, mitochondrial and organelle membranes, as well as metabolic, especially biosynthetic, processes (Figure 7B ).
The functional network analysis based on 𝜅-Score ≥ 0.4 for differentially expressed GO terms with FDR ≤ 0.05 in the DEP treatment shows clustering to specific functional groups (Figure A6A ). Upregulated functions are related to phosphorylation, regulation of metabolic process, guanyl nucleotide binding, and signal transduction (Figure A6B ). Downregulated functions are related to mitochondria, lipid metabolic processes, the endoplasmic reticulum, and phospholipid biosynthetic processes (Figure A6C ).