Fig. 2: Gene expression analysis of SNc in MPTP-induced PD mice treated with Withaferin A.

A Hierarchical clustered heatmap of gene expression profiles for WA or vehicle treatment in SNc of MPTP-induced PD mice. B Heatmap of DEGs of MPTP-received mice treated with WA or vehicle. C Scatter plot highlights the DEGs of WA treatment compared with vehicle in MPTP-recieved mice, upregulated genes are colored in red, downregulated genes are colored in blue. (P < 0.05 with unpaired two-tailed Student’s t tests). D Gene Ontology enrichment was based on DEGs that have a P value smaller than 0.05. Enrichment analysis for Gene Ontology terms among the genes of a gene–trait correlation module was performed using Metascape. E Volcano plot displays DEGs of WA treatment compared with vehicle in MPTP-received mice. Significantly altered genes are colored in red, insignificantly altered genes are colored in blue. F Venn diagram of overlapping significantly changed genes (±1.2 fold, P < 0.05). The top ten overlapping genes are presented. G Protein–protein interaction network identified among DJ1, Nrf2 and STING using GeneMANIA (direct interaction database). H Representative immunoblots of DJ1, Nrf2, STING and β-actin, and quantification of DJ1, Nrf2, STING protein levels in SNc (cropped blot images are shown, see Supplementary Fig. 16 for full immunoblots). Data are mean±s.e.m.; n = 9 biologically independent animals; *P < 0.05, **P < 0.01, and ***P < 0.001. I Relative mRNA expression of the indicated genes in SNc. Data are mean ± s.e.m.; n = 8 biologically independent animals. The one-way ANOVAs were used for statistical analysis followed by Bonferroni’s post hoc test. *P < 0.05, **P < 0.01, and ***P < 0.001. J Heatmap of the top 100 significant genes of SNc of human PD samples analyzed by Meta-analysis (FDR < 0.05). Expression values of each gene are standardized within each dataset. Hierarchical clustering was used to cluster samples and genes.