Protein–Protein Interaction (PPI) Network

The targeted genes were further analyzed at the protein level using protein-protein interaction network functional enrichment analysis through STRING (Protein-Protein Interaction Network Functional Enrichment Analysis) (https://string-db.org/). Results from STRING were further analyzed using Cytoscape to visualize molecular interaction networks and integrating gene expression profiles to identify clusters of protein interaction that are highly related to the pathogenesis of CML. The gene interaction relationship was downloaded in the “TSV” format file and was imported into the Cytoscape software (http://www.cytoscape.org/) for further analysis and clustering. The Cytoscape MCODE plug-in was employed to perform module analysis of the target network and protein clustering. The module selection criteria were as follows: degree cutoff = 2, node score cutoff = 0.2, node density cutoff = 0.1, K-score = 2, and max depth = 100. The list of genes in the cluster was then analyzed again using DAVID for significantly enriched ontology terms.