4.5.3. Functional Enrichment Analysis of the Key Module

We performed GO and KEGG enrichment analysis for key modules with most genes by using the Database for Annotation, Visualization and Integrated Discovery (DAVID, https://david.ncifcrf.gov/ summary.jsp) [60] and KEGG Orthology Based Annotation System (KOBAS, https://bio.tools/kobas). Analysis results were extracted out under the condition of *p* < 0.05 after correction [61,62].

#### 4.5.4. Identification of Hub Genes

The hub gene is usually used as an abbreviation for a highly connected gene, which has a high degree of connectivity in co-expression modules. Module membership (MM) is defined as the correlation between the expression of each gene and its module eigengenes (MEs). Gene significance (GS) is defined as the correlation of each gene to the trait of interest. In the module of interest, the genes with the highest MM and GS were set as candidate genes for further analysis [63]. We chose the intramodular hub genes by external traits based GS > 0.2 and MM > 0.8 with a threshold of *p*-value < 0.05 [64]. In our study, based on the size of the module, we classified the top 10% of the most connected genes in the module as hub genes. We construct and visualize gene–gene interaction networks using Cytoscape tool [65].
