fig4

Figure 4. TCGA gene module analysis. (A) Soft-threshold selection. The left plot shows the optimal soft threshold as the first value exceeding the red line, and the right plot typically shows the optimal soft threshold at the point of inflection. The best soft threshold chosen here is 3; (B) WGCNA hierarchical clustering. The top part shows the hierarchical clustering tree, and the bottom part shows the modules corresponding to genes, with each color representing a different module, and the gray module representing an ineffective module; (C) Heatmap of inter-module gene correlations; (D) Heatmap of associations between WGCNA gene modules and sample group labels, displaying the correlations and P-values in parentheses; (E) Bubble plot of KEGG enrichment results. The color indicates the corrected P-value, with smaller P-values closer to red, signifying greater significance; (F) Bar plots of GO enrichment results. TCGA: The Cancer Genome Atlas; WGCNA: weighted gene co-expression network analysis; EKGG: Kyoto Encyclopedia of Genes and Genomes; GO: Gene Ontology.