Identification of DEGs in bone tissues from diabetic mice
To determine the effects of liraglutide on the bone from the diabetic mice, we analyzed the RNA-seq data from bone tissues with the treatment of liraglutide. A total of 620 genes were identified with the threshold of P < 0.05. The up-and-down-regulated genes were shown by the heatmap and volcano plot (Figure 1). The top ten DEGs were selected in Table 1.
KEGG and GO analyses in bone tissues from diabetic mice
To determine the mechanism of liraglutide-regulated bone in diabetic mice, we applied the KEGG and GO analyses (Figure 2). We identified the top ten KEGG signaling pathways, including “Coronavirus disease − COVID−19”, “Ribosome”, “Diabetic cardiomyopathy”, “Amyotrophic lateral sclerosis”, “Chemical carcinogenesis −reactive oxygen species”, “Thermogenesis”, “Parkinson disease”, “Oxidative phosphorylation”, “Non−alcoholic fatty liver disease”, and “Cardiac muscle contraction”. We identified the top ten biological processes, including “Generation of precursor metabolites and energy”, “Energy derivation by oxidation of organic compounds”, “Cellular respiration”, “ATP metabolic process”, “Aerobic respiration”, “Oxidative phosphorylation”, “Respiratory electron transport chain”, “Electron transport chain”, “Regulation of cardiac muscle hypertrophy”, and “Regulation of muscle hypertrophy”. We identified the top ten cellular components, including “Organelle inner membrane”, “Ribosome”, “Mitochondrial inner membrane”, “Cytosolic ribosome”, “Ribosomal subunit”, “Large ribosomal subunit”, “Cytosolic large ribosomal subunit”, “Inner mitochondrial membrane protein complex”, “Mitochondrial respirasome”, and “Cytosolic small ribosomal subunit”. We also identified the top ten molecular functions of GO, including “Structural constituent of ribosome”, “Active transmembrane transporter activity”, “Secondary active transmembrane transporter activity”, “Active ion transmembrane transporter activity”, “Kinase regulator activity”, “Proton transmembrane transporter activity”, “rRNA binding”, “Ubiquitin−protein transferase regulator activity”, “Ubiquitin ligase inhibitor activity”, “Ubiquitin−protein transferase inhibitor activity”.
PPI networks in bone tissues from diabetic mice
To determine the interaction among the DEGs, we constructed the PPI networks by using the Cytoscape (combined score > 0.4). Table 2 showed the top ten interactive molecules with the highest degree scores. The top two modules were indicated in Figure 3. We further determined the mechanisms with Reactome map (Figure 4) and identified the top ten significant processes including “Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)”, “Formation of a pool of free 40S subunits”, “Viral mRNA Translation”, “SRP-dependent cotranslational protein targeting to membrane”, “GTP hydrolysis and joining of the 60S ribosomal subunit”, “L13a-mediated translational silencing of Ceruloplasmin expression”, “Nonsense-Mediated Decay (NMD)”, “Peptide chain elongation”, “Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)”, and “Eukaryotic Translation Initiation” (Supplemental Table S1).