Fig. 2
WGCNA and functional enrichment analysis. (A) Analysis of sample clustering and identification of outliers. (B) Scale-free fit index analysis across different soft threshold powers (β). (C) Dendrogram cut at a height of 0.25 to detect and merge similar modules. (D) Original and merged modules under the dendrogram. (E) Heatmap of module-trait relationships, with each cell displaying the corresponding correlation and p-value. (F) Bar graph showing gene significance across different modules. (G) Venn diagram illustrating the intersection between differentially expressed genes and key gene modules identified by WGCNA. (H) Bubble chart displaying the KEGG enrichment analysis results for the intersected gene set. (I) Bubble chart presenting the GO enrichment analysis results for the intersected gene set. (J) Circular plot showing the GO enrichment analysis results for the intersected gene set, including annotations for each enriched pathway. GO:0071229: cellular response to acid chemical; GO:0030199: collagen fibril organization; GO:0071230: cellular response to amino acid stimulus; GO:0001101: response to acid chemical; GO:0061326: renal tubule development; GO:0030198: extracellular matrix organization; GO:0098644: complex of collagen trimers; GO:0005583: fibrillar collagen trimer; GO:0098643: banded collagen fibril; GO:0062023: collagen-containing extracellular matrix; GO:0005788: endoplasmic reticulum lumen; GO:0005581: collagen trimer; GO:0005201: extracellular matrix structural constituent; GO:0030020: extracellular matrix structural constituent conferring tensile strength; GO:0048407: platelet-derived growth factor binding; GO:0019838: growth factor binding; GO:0042805: actinin binding; GO:0099094: ligand-gated monoatomic cation channel activity. All images were created using R software (version 4.3.1, https://www.r-project.org). Statistical significance is denoted as *p < 0.05, **p < 0.01, ***p < 0.001.
