Pathway enrichment results
The network analysis highlighted a total of 14 genes with a relevant node degree score. Figure 3 shows the “seedGeneNetwork” with the key interactions among the 14 seed genes and other genes involved in several canonical pathway.
The seed genes enriching multiple pathways highlighted the relationships between seed genes and the affected biological functions involved in HCC and sorafenib. Among all genes, ADH1A and CYP26A1 , along with VEGF-A and VEGF-C , showed a common involvement in the signal transduction pathways, which are reported as dysregulated in HCC, leading to uncontrolled cell division and metastasis.34
Table 3 reports the top 21 degree-ranked seed genes among which, with a high degree value, are included 8/12 genes identified in the study (in bold). Analyzing Table 4, it is worth noting that a seed gene’s degree is higher than the added genes and refers to the centrality of a node in the network. The higher centrality of the degree reveals the crucial roles of genes in the network. Figure 4 shows the top ten degree-ranked seed genes computed using CytoHubba.