Differential Gene Expression Analysis

The differentially expressed genes between the high and low IRRS groups were analyzed using the DESeq2 package, with threshold |log2 fold change (FC)| ≥2 and Benjamini–Hochberg-adjusted P-value<0.05 (30 (link)). Functional enrichment analysis and clustering of the identified biological processes were conducted using the clusterProfiler R package (31 (link)).
The main regulator (MR) is a gene located at the hub of a regulatory network that controls a large number of target genes (termed as its regulon). We used the MR4Cancer tool (http://cis.hku.hk/MR4Cancer) to identify potential MRs that could explain the DEGs between the high and low IRRS groups (32 (link)). An MR network diagram was drawn using Cytoscape.