Figure 2. PRMT5 inhibition leads to the up-regulation of MYC and p53 pathways.

(A) MA plot of differential gene expression results. The x-axis represents the mean expression levels of genes, whereas the y-axis shows the log₂ fold changes (LFC) between conditions. Genes that are significantly differentially expressed (adjusted P-value < 0.05) are highlighted in red. (B) Volcano plot of differential gene expression results. The x-axis shows LFC, and the y-axis shows −log₁₀ (adjusted P-value). Genes with |LFC| > 1 and P < 0.05 are in red; those not meeting P-value or LFC thresholds are in blue and green, respectively; others are in gray. Gene labels were automatically selected by the EnhancedVolcano R package, which prioritizes the most statistically significant and highly differentially expressed genes and places as many labels as possible without overlapping. (C) Normalized enrichment score (NES) values for significantly up- and down-regulated pathways from the gene set enrichment analysis using the MSigDB hallmark gene sets. Pathways up-regulated in PRMT5-inhibited samples are shown in red, whereas down-regulated pathways are shown in blue. (D) Gene set enrichment analysis enrichment plots for the top two up-regulated pathways: MYC Targets V1 and P53 Pathway. Each plot displays the ranked gene list scores and enrichment score (ES) curve. Ranked gene lists were obtained from differential gene expression results and ordered by the Wald statistics, which is the ratio of the logFC to standard error.