Transcriptomics analysis of pex1 larvae indicates ER stress, alteration of neurological and visual processes, and dysregulation of bile acid metabolism. (A) Partial Least Squares Discriminant Analysis (PLS-DA) of gene transcripts of 11 dpf WT and pex1–/– larvae. Each dot represents a single biological replicate of a pool of ten WT (gray) or pex1–/– (orange) larvae. (B) Volcano plot showing significantly altered genes (adj. p-value < 0.01) in red, strongly downregulated genes (log2FC ≤ –1.5) in gray, and strongly upregulated genes (log2FC ≥ + 1.5) in blue. (C) Summary bar plot of the number of DEGs identified by the transcriptomics analysis. (D) qPCR validation of selected DEGs identified by RNAseq. All expression levels in pex1–/– larvae are shown relative to WT levels. (E) Dot plot showing cellular process networks significantly enriched in differentially expressed genes. Dot position along the x-axis represents -log10(minFDR) values, with dots further right indicating higher statistical significance as measured by the false-discovery rate (FDR). Dot size reflects the number of genes found in each process, and color intensity indicates significance level. Processes related to protein folding and endoplasmic reticulum stress pathways show the strongest enrichment signals.
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