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.