3.3 Candidate miRNA-mRNA pairs
A total of 787677 candidate miRNA-mRNA pairs were predicted using
miRanda, Targetscans, and Pictar. Among these pairs, only the
upregulated miRNA-downregulated mRNA pairs or downregulated
miRNA-upregulated mRNA pairs were further selected based on the miRNA
and mRNA expression profile data in Section 3.1 (E-Table 1, E-Table 2).
Thus, a total of 3827 candidate miRNA-mRNA pairs were selected, and 83
miRNAs were involved. Among them, miRNA-374 had the largest number of
targets (142 targets), and the gene 2810055g20 Rik was regulated by the
most number of (29 miRNAs in total). The top 10 miRNA and mRNA were
shown in Table 3.
Next, GO and KEGG function enrichment pathway analyses were performed on
predicted targets of each differentially expressed miRNA. Some
miRNAs-regulated targets were significantly enriched in immune
regulation and inflammation-related functions, such as let-7f, miR-205,
and miR-21 (Figure 3A-C). Correspondingly, the immune and
inflammation-related genes were predicted to be downregulated, which was
in agreement with the GO and KEGG function enrichment results for
downregulated differentially expressed genes (Figure 2A, 2B, E-Table 5,
E-Table 6). These miRNA-mRNA pairs are believed to play a role in
biological and pathological mechanisms of BPD.