Fig. 5

Multi-omics derived gene regulatory network (A), Intersection among the 1858 genes selected for network analyses. Network genes were divided into 7 categories: differentially expressed genes (DEG), differentially expressed genes/promoters (DMG, DMP), differentially accessible regions (genic and promoter regions as DAC), genes harboring SNPs reported in literature as being associated with salmon maturation (SNP), tissue-specific genes (TS) and key regulators identified by RIF (TF). The nature of a given intersection is indicated by the dots below the bar plot. For example, the 442 genes in the second column are both differentially methylated and differentially expressed but not found in other categories (B), Enriched gene ontology (GO) terms (hypergeometric test, Bonferroni-adjusted P < 0.05) among the list of 1858 network genes (C), Gene regulatory network constructed using the PCIT algorithm, for visualization only nodes with significant correlations ≥ ±0.95 (929 genes with 17,708 connections) were considered. All nodes are represented by ellipses except for genes coding key regulators (TFs) have diamond shape. Nodes with yellow borders are differentially methylated, whereas nodes with white labels are differentially accessible. Node colours are relative to the tissue of maximum expression with blue represents the pituitary, red represents ovary and green represents liver. The size of the nodes is relative to the normalized mean expression values in all samples. Connectivity structures of the 1858 network genes used to build the network are shown