Identification and Analysis of Shared DEGs and Hub Genes

By writing an R script, we compared the DEGs of two GSE samples and identified the shared DEGs (including upregulated, downregulated, and reversed expressions). Then, we employed unsupervised hierarchical clustering and expression correlation calculations based on the shared DEG series matrix file and plotted them with the R package ggplot2. The Annotation, Visualization, and Integrated Discovery Database (DAVID, v6.8, https:/david.ncifcrf.gov/) was employed to conduct Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. A modified Fisher's exact test, the p-value (or EASE score), was used to examine the significance of gene ontology/KEGG pathway term enrichment. The Benjamini–Hochberg procedure was used to correct the p-values of individual term member enrichment globally. These gene ontology/pathway terms with a p-value cutoff ≤0.05 and Benjamini–Hochberg cutoff ≤0.5 were regarded as significant and interesting.

In the present study, the PPI network of shared DEGs was constructed using the STRING database, and interaction with a combined score >0.4 was regarded as statistically significant. Subsequently, engaging the Network Analyzer plugin in Cytoscape, the network topology parameters were analyzed to obtain the average shortest path length (ASPL), betweenness centrality (BC), etc., and nodes with a shorter ASPL and higher BC were considered as hub genes (Assenov et al., 2008; Li et al., 2018).