Figure 3

Weighted gene co-expression network analysis (WGCNA). (a) Correlation between module and trait. (b–d) Volcano plot for comparing gene expression between IVI + MT and IVI in the blue, green, and turquoise modules. Blue indicates a significant decrease in gene expression in IVI + MT relative to IVI at P < 0.05 and fold change (FC) < 0.67; red indicates a significant increase in gene expression in IVI + MT relative to IVI at P < 0.05 and FC > 1.5. (e) Summary of cell type enrichment analysis (CTen). –log₁₀ Benjamini–Hochberg adjusted P > 2 was considered to be significant. For each module, the left column shows the results using all genes in the module; the right column shows the results using genes significantly increased by MT relative to IVI. (f) Pathway enrichment analysis of differentially expressed genes between IVI and NI in the blue (FDR < 0.05) (f1) and green (major top 7 pathways with FDR < 0.05) (f2) modules. The gene sets significantly increased by IVI relative to NI at criteria of P < 0.05 and log₂FC > 3 were used for analysis. (g) Pathway enrichment analysis of differentially expressed genes between IVI + MT and IVI in the green (FDR < 0.05) (g1) and turquoise (FDR < 0.05) (g2) modules. The gene sets significantly increased by MT relative to IVI at criteria of P < 0.05 and FC > 1.5 were used for analysis.