Fig. 3: Co-expression analysis for screening core genesets.

a Scale independence vs. soft threshold (power): The plot shows the relationship between the scale-free topology model fit and the soft threshold (power) used in weighted gene co-expression network analysis (WGCNA). A soft threshold of 6 was chosen based on the highest value, ensuring a scale-free network topology. b Mean connectivity vs. soft threshold (power): This plot illustrates the mean connectivity of genes in the network as a function of the soft threshold. A soft threshold of 6 was selected to balance the scale-free topology and mean connectivity. c Cluster dendrogram of genes: The hierarchical clustering dendrogram shows the co-expression modules identified by WGCNA. Genes are grouped into modules based on their expression patterns. The module colors are displayed at the bottom, with each color representing a distinct gene module. d Module-trait relationships: The heatmap shows the correlation between the identified WGCNA modules (rows) and the trait of interest (Cuptosis-related genes, column). Positive and negative correlations are shown in blue and red, respectively, with statistical significance (p-value) indicated on the right. The blue modules (e.g., MEcyan, MEturquoise) show significant positive correlations, while other modules exhibit weaker or no significant relationships. e Module membership vs. gene significance for Cuptosis-related genes: The scatter plot demonstrates the correlation between module membership (i.e., the degree of a gene’s association with a given module) and the gene significance for Cuptosis-related genes. A positive correlation (cor = 0.37, p = 1.9e-30) indicates that genes in the blue module are highly associated with the Cuptosis-related trait. f Venn diagram of WGCNA module genes and uni-cox regression results: The Venn diagram shows the overlap between the genes identified by WGCNA (896 genes) and those selected through uni-cox regression (4260 genes). The intersection (85 genes) represents genes that are common to both analyses, highlighting potential key genes related to Cuptosis.