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 ).