STRING Network Analysis

Significantly upregulated mRNAs (2,777 genes; p < 0.05) identified by bulk RNA-seq were analyzed using the STRING module in Cytoscape v.2.2.0 (Institute for System Biology; WA; USA). A cluster network was constructed using the MCL algorithm with a granularity parameter of 4, followed by filtering nodes with mcl.cluster > 10. The resulting 1,848 nodes were processed through STRING v12.0 (Swiss Institute of Bioinformatics; Lausanne; Switzerland) to generate a protein–protein interaction (PPI) network, incorporating evidence from text mining, genomic neighborhood, experimental data, curated databases, co-expression, gene fusion, and co-occurrence, with a minimum confidence score threshold of 0.40. Network modules were defined using the DBSCAN clustering algorithm with an ε parameter of 2. Cluster 1, representing the largest gene set (101 genes), was further analyzed by sorting the top 20 nodes with the highest node degree, resulting in a network comprising 101 nodes and 756 edges. Global network metrics indicated an average node degree of 15, a local clustering coefficient of 0.600, and a PPI enrichment p-value of < 1 × 10⁻¹⁶. The average values of coexpression, experimentally determined interactions, automated text mining, and combined scores were calculated.