Protein Interaction Network Analysis

An online database of known and predicted protein interactions, Search Tool for the Retrieval of Interacting Genes (STRING; http://string-db.org; version 10.0), was applied to predict the PPI network of DEGs (Franceschini et al., 2013 (link)) while interactions with a combined score > 0.4 were taken as statistically significant. Cytoscape (version 3.6.1, http://www.cytoscape.org; Smoot et al., 2011 (link)) was used to visualize molecular interaction networks, specifically using its plug-in CytoNCA to analyze the topological properties of nodes in the PPI network with parameters set as unweighted. By ranking the scores of each node, we obtained important nodes of protein interactions within the network. Considering most networks were scale-free, the hub genes with degree ≥ 20 were selected. Metascape³ was used to further verify the function enrichment of hub genes (Zhou et al., 2019 ) with P-value < 0.05 as the cutoff. Hub genes pathway analysis was performed and visualized by ClueGO (version 2.5.4) and CluePedia (version 1.5.4), also plug-ins of Cytoscape. P-value < 0.01 was considered to be statistically significant. A network of genes and their co-expression genes was analyzed via GeneMANIA⁴ (Warde-Farley et al., 2010 (link)). Finally, the expression of identified hub gene was verified in GSE14905 dataset.