fig3

Figure 3. Integrated presentation of transcriptomic and metabolomic analyses. (A) FPKM density distribution of transcript expression across samples; (B) Pearson correlation heatmap showing reproducibility among replicates; (C) PCA scatter plot illustrating global expression differences; (D) Hierarchical clustering of DEGs; (E) Volcano plot showing upregulated, downregulated, and unchanged genes. Differential expression analysis was performed using DESeq2 based on raw read counts. Statistical significance was assessed using the Wald test, and P values were adjusted using the Benjamini-Hochberg procedure to control the FDR. Genes with |log₂FC| > 1 and an adjusted P value (FDR) < 0.05 were considered DEGs; (F) GO enrichment bubble plot for BP, MF, and CC; (G) KEGG pathway enrichment bar chart of the top 20 significantly enriched pathways. GO and KEGG enrichment analyses were performed using Fisher’s exact test, with P values adjusted using the Benjamini-Hochberg procedure. BP: Biological process; CC: cellular component; DEGs: differentially expressed genes; FDR: false discovery rate; FPKM: fragments per kilobase of transcript per million mapped reads; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; log₂FC: log₂ fold change; MF: molecular function; PBS: phosphate-buffered saline; PCA: principal component analysis; TWELP: Tripterygium wilfordii-derived exosome-like nanoparticles; TWELP@GlcN-HA: engineered Tripterygium wilfordii-derived exosome-like nanoparticle system.