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 ).