Fig. 4.

Gene Ontology and protein–protein interaction network analysis of genes exhibiting differential expression in wild-type and GR-mutant brains. (A) REVIGO TreeMap produced with a REVIGO-generated R script by using the Biological process terms identified with the Gene Ontology (GO) enrichment analysis and visualisation (GOrilla) tool (threshold P-value set to <10⁻⁵), which are linked to transcripts exhibiting differential expression in wild-type and GR-mutant adult brain transcriptomes (n=6 fish, for each genotype). (B) Dot Plot using the enrichGO function within the clusterProfiler R package to identify Biological process GO terms linked to transcripts exhibiting differential expression in wild-type and GR-mutant adult brain transcriptomes (q-value cut-off was 0.05). The circle diameter indicates the number of genes linked to a specific GO term (count number). The gene ratio is the percentage of the total number of differentially expressed genes linked to a specific GO term. (C) UpSet Plot using the enrichGO function within the clusterProfiler R package to identify intersections between Biological process GO term-linked gene sets that exhibit differential expression in wild-type and GR-mutant adult brain transcriptomes. Indicated on the y-axis are the number of genes found in the GO categories. (D–F) STRING protein–protein interaction networks of proteins encoded by GR-regulated genes under the GO terms ‘chaperone-mediated protein folding’ (D), ‘circadian rhythm’ (E) or ‘regulation of primary metabolic process’ (F), respectively indicating interactions between many protein chaperones, circadian clock transcription factors or circadian clock transcription factors and immediate-early transcription factors. Individual proteins are nodes, edges are links between proteins signifying the various interaction data that support the interactions, all colouring is according to evidence type (see von Mering et al., 2007) and STRING website for colour legend.