4. Discussion
We constructed 145 negative miRNA-mRNA-protein pairs in P. vachelli muscle induced by hypoxia (Table S4) , and later discovered that 16 DEMI, 23 DEG/DEP and 17 DEM were involved in 19 mutual KEGG pathways (Table S5) . The predicted miRNA-mRNA-protein-metabolite regulatory networks were more complex than previously thought. A single miRNA could regulate multi-target mRNAs/proteins/metabolite and vice versa (Fig. 4 ). In performing KEGG pathway analyses for DEG/DEP and multi-omics pairs, “signal transduction”, “metabolism” and “muscle function” were found to be the three most frequently represented subclasses (Fig. 2 and Fig. 3 ). With regard to the fish hypoxia adaptation strategy, we highlighted our particular research using pathway analysis related to the functional clusters: 1. HIF-1 signaling pathway; 2. Energy metabolism; 3. Muscle function. Some DEG and their regulating miRNAs among above clusters representing hypoxic markers were further analyzed using qRT-PCR (Table 1, Fig. 5and Fig. 6 ).