For network analysis, the gene list was filtered using a log2 FC HAP relative to LAP cut-off of ≥±0.5, which resulted in 485 significant differential expressed genes between lines. Of the 485 genes submitted for interaction analysis in String-db, 187 edges were discovered compared to an expected number of 158 edges (Figure 2; enrichment p=0.0126). Using Cytoscape’s CytoHubba, 8 hub genes were found in this differential gene expression network (See Supplementary File “Enrichment.Hubs_RNASeq” for full details on hub genes for network of differentially expressed genes) with the top five hub genes presented in Table 2 (also highlighted in orange text in Figure 2). Of these, Ubc displayed the greatest degrees, whereas Ccl6 and Ccl9 showed the greatest MCC. Although no KEGG or Reactome pathways were enriched in this network, the assessment of GO revealed 15 cellular components (CC), 137 biological processes (BP), and 3 molecular functions (MF) that were enriched in the network of differentially expressed genes submitted to String-db (See Supplementary Files for full details on significantly enriched GO terms for network of differentially expressed genes). In particular, immunity-related
