Of every node inside the ceRNA skeletal muscle improvement, we calculated
Of every node within the ceRNA skeletal muscle improvement, we calculated the connectivity of each node within the ceRNA network employing Gephi software program. The top 5 lncRNAs together with the JPH203 Autophagy highest connectivity degree application. The top 5 lncRNAs together with the highest connectivity network using degree were classified hub lncRNAs, like TCONS_00066712, TCONS_00026594, have been classified as as hub lncRNAs, including TCONS_00066712, TCONS_00026594, TCONS_00001557, TCONS_00001553, and TCONS_00003307 (Figure five). Each of the 5 hub TCONS_00001557, TCONS_00001553, and TCONS_00003307 (Figure 5). Each of the five hub lncRNAs had been highly expressed through the embryonic stage and then were downregulated with skeletal muscle improvement (Figure 6A). The five hub lncRNAs interact with 29 miRNAs and 404 mRNAs, forming 1332 lncRNA iRNA RNA ceRNA interactions (Table S13). We then performed KEGG enrichment analysis on the 404 mRNAs targeted by the 29 miRNAs in the ceRNA network (Table S14). In total, 11 KEGG pathways have been drastically enriched, containing cell cycle, spliceosome, and nucleocytoplasmic transport. Cell cycle was the leading enriched pathway consisting of 12 genes of ABL proto-oncogene 1, non-receptor tyrosine kinase (ABL1), cyclin B2 (CCNB2), cell division cycle 16 (CDC16), cell division cycle 27 (CDC27), histone deacetylase 1 (HDAC1), mini-chromosome maintenance complicated component six (MCM6), origin recognition complex subunit two (ORC2), RAD21 cohesin complex component (RAD21), RB transcriptional corepressor like 1 (RBL1), tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta (YWHAB), tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon (YWHAE), and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta (YWHAQ). It was also found that lots of muscle-specific miRNAs interacted together with the five hub lncRNAs, such as cli-miR-133a-3p, cli-miR-133a-5p, and cli-miR-1a-3p, producing 136 lncRNA iRNA RNA interactions (Figure 5). These 136 interactions had been identified as possible vital ceRNA pairs regulating Sutezolid Epigenetic Reader Domain pigeon skeletal muscle improvement.Genes 2021, 12, 1787 x FOR PEER Review Genes 2021, 12,12 of 1910 ofFigure 5. Visualization of mRNA, vital lncRNA iRNA RNA interactions. Red, green, and blue nodes represent lncRNA, miRNA, and Genes 2021, 12, x FOR PEER Assessment the 136 respectively. Pink nodes represent the ceRNA interactions validated by dual-luciferase lncRNA, miRNA, and mRNA, respectively. Pink nodes represent the ceRNA interactions validated by dual-luciferase assay. assay. The node size is proportional for the connectivity degree. The node size is proportional to the connectivity degree.Figure five. Visualization in the 136 critical lncRNA iRNA RNA interactions. Red, green, and blue nodes represent13 ofFigure 6. Cont.Genes 2021, 12,11 ofFigure 6. Identification prospective lncRNA iRNA RNA interactions in pigeon skeletal muscle improvement: (A) exFigure six. Identification of of possible lncRNA iRNA RNA interactions in pigeon skeletal muscle development: pression profiles of theof the fivelncRNAs throughout skeletal muscle development; (B) correlation analysis of expression pro(A) expression profiles five hub hub lncRNAs through skeletal muscle development; (B) correlation evaluation of expression files of the 5 hub lncRNAs and three muscle-specific miRNAs detected by RNA-seq and qRT-PCR. p 0.05 indicates profiles from the five hub lncRNAs and three muscle-specific miRNAs detected by RNA-seq and qRT-PCR. p 0.05 indic.