Protein Interaction Network Analysis

Using the online STRING (http://string-db.org/) database [12 (link)], which is a biological database and web resource for known and predicted PPIs, we developed a network of DEG-encoded proteins and PPIs. Cytoscape software [13 (link)] was applied to visualize the protein interaction relationship network and analyze hub proteins, which are important nodes with many interaction partners. We utilized the CytoHubba application in Cytoscape, employing five calculation methods: Degree, EPC, EcCentricity, MCC, and MNC. The intersecting genes derived using these five algorithms encode core proteins and may represent key candidate genes with important biological regulatory functions. ClusterONE, an application in Cytoscape, was utilized to identify the crucial modules for further analysis. ClueGO and CluePedia were also employed to draw KEGG pathways for visualization purposes.