Fig. 5.

Differential gene expression in thedj-1^−/− mutant brain. (A) A volcano plot representing the global changes in gene expression observed by RNA-seq analysis, comparing RNA from the brains of dj-1^−/− mutants (n=3, biological replicates) and their wild-type siblings (n=3) at 16 wpf. The fold change (log2) of each transcript was plotted against the P-value (−log10). Transcripts in red are down/upregulated less than 2-fold. Transcripts in orange that appear above the dotted line are differentially expressed with a P-value of <0.05 and down/upregulated more than 2-fold. Transcripts in blue have a P-value of ≥0.05. (B) A heatmap showing select genes differentially expressed with an FDR q-value of <0.05. Relative expression is represented on a colour scale from blue (low) to orange (high). (C) qRT-PCR analysis validating the results seen in the RNA-seq using RNA extracted from the brains of dj-1^−/− and wild-type siblings at 16 wpf (n=3 for all but n=5 for kcnk analysis, biological replicates). Student's t-tests (two-tailed, unpaired) were used to compare the dCt values for dj-1^−/− and wild-type samples. Data are mean±s.e.m., *P<0.05, **P<0.01, ***P<0.001. (D) GSEA enrichment plots for Hallmark gene sets: G2M checkpoint, oxidative phosphorylation, E2F transcription factors and PI3K/AKT/mTOR signalling. FDR, false discovery rate-adjusted P-value; NES, normalised enrichment score; P, nominal P-value. Data have been deposited in GEO, accession number GSE135271.