Fig. 2
PCA and differential expression analysis of PD and PMOP datasets (A) Principal component analysis (PCA) of PMOP (n = 10, orange) vs. control (n = 3, green) transcriptomes. Partial group overlap shown by 95% confidence ellipses (PC1: 38.38%, PC2: 17.49%). (B) PD (n = 241, orange) and control (n = 69, green) transcriptomes. Partial group overlap shown by 95% confidence ellipses (PC1: 20.82%, PC2: 13.74%). (C) Volcano plot of PMOP vs. control groups identifies 794 upregulated (orange) and 443 downregulated (green) genes (|log₂FC|> 1.5, FDR < 0.05). Gray dots denote non-significant transcripts. Thresholds marked by dashed lines (vertical: fold change; horizontal: − log₁₀[p value]). (D) PD vs. control analysis reveals 771 upregulated (orange) and 473 downregulated (green) DEGs under identical thresholds. Top 5 ranked DEGs by fold change are labeled (black text).
