3.3 Correlation of miRNA-mRNA-protein regulatory network
348 conserved miRNAs belonging to 292 miRNA seed-based families were
identified in the six small RNA
libraries (M0a, M0b, M0c, M4a, M4b, and M4c). The quality control
analysis of the miRNAome is shown in Table S3 , including
overview of reads from raw data to cleaned sequences, summary of known
and predicted miRNA, length distribution of sequences, and conservation
of the identified miRNA with other species. A total of 39 differentially
expressed miRNAs (DEMI) were found (P < 0.05), with 17
upregulated and 22 downregulated miRNAs (Table S2 ).
In our results, according to the DEMI, DEG and DEP datasets and
miRNA-targeting information, 1809 negative miRNA-mRNA regulatory network
with the expression pattern of up-down and down-up were detected
(Table S4 ). Further, 12 of 20 significant enriched KEGG
pathways for 1809 pairs were found to be overlapping for those of
transcriptome, also involved in vessel formation, metabolism, immune
response and muscle dysfunction. Additionally, similar to the DEG, the
numbers of upregulated genes were greater than that of downregulated
ones involved in vessel formation, catabolism, immune response, muscle
dysfunction, and vice versa for anabolism (Fig. 3A ). Finally we
identified 145 negative miRNA-mRNA-protein pairs (up-down-down and
down-up-up) with negative
correlation as the key for analysis including 21 DEMI and 60
co-DEG/DEP in total (Fig.
4A ). Moreover, five out of 11 significant enriched KEGG pathways for
145 pairs were found to be overlapping for those of proteome, such as
“Citrate cycle (TCA cycle)”, “Oxidative phosphorylation”,
“Tryptophan metabolism”, “Glyoxylate and dicarboxylate metabolism”,
and “Galactose metabolism”, with carbohydrate metabolism of the most
commonly represented subclasses. In addition, biosynthesis related to
“Butirosin and neomycin
biosynthesis” and “Protein
export” were significantly enriched by down co-DEG/DEP (Fig.
3B ).