mples was pretty much on the similar line and close to 0 (Figure 1), indicating

mples was pretty much on the similar line and close to 0 (Figure 1), indicating superior quality of standardization. In the 1-day time-point, within the BIT group, 222 genes have been upregulated in comparison using the BI group, in which 148 genes had been downregulated. At the 2-day time-point, inside the BIT group, 328 genes were upregulated in comparison with the BI group, in which 375 genes have been downregulated. At the 3-day time-point, the corresponding numbers had been 533 upregulated and 515 downregulated, and at the 7-day time-point, the corresponding numbers were 786 upregulated and 754 downregulated. The DEGs in the 4 time-points were combined, as well as the overlap of theFrontiers in Genetics | frontiersin.orgNovember 2021 | Volume 12 | ArticleDu et al.Crucial Genes of Osteogenic and Adipogenic DifferentiationFIGURE 2 | Venn diagrams displaying (A) the 98 upregulated genes and (B) the 66 downregulated genes. A differentially expressed gene (DEG) volcano plot (C) along with a heatmap (D) are shown. Red represents upregulated genes, and green represents downregulated genes (p 0.05, logFC 1 or logFC -1).pathways. Despite the fact that the p-value of “sa05200: Pathways in cancer” was 0.05, it contained a large number of enriched genes.Protein rotein Interaction Networks of the Differentially Expressed Genes and Identification of Hub GenesTo systematically analyze the PPIs of DEGs, PPI networks of the upregulated and downregulated genes have been constructed utilizing Cytoscape software (Figures 4A,B). Within the PPI networks from the upregulated genes, the DEGs with all the highest connectivity degrees had been BMP2, CTGF, IGF1, TGFB3, MMP13, MMP3, SERPINE1, COMP, ASPN, and IL11. Similarly, within the PPI networks of upregulated genes, the DEGs together with the highest connectivity degrees were PPARG, TIMP3, ANXA1, ADAMTS5, TIMP4, AGTR1, NQO1, CXCL12, CEBPA, and CFD. The PPI networks of the DEGs from theSTRING database had been deposited into Cytoscape v3.7.two, then the cytoHubba plugin from Cytoscape was utilized to recognize hub genes in the PPI networks, and hub genes overlapped by MCC, MNC, and Degree. The top rated seven upregulated hub genes had been CTGF, IGF1, BMP2, MMP13, TGFB3, MMP3, and SERPINE1; as well as the top rated seven downregulated hub genes have been PPARG, TIMP3, ANXA1, ADAMTS5, AGTR1, CXCL12, and CEBPA (Figures 4A,B).Hub Gene mRNA Expression Levels and ValidationmRNA expression levels of upregulated hub genes involved in osteogenic differentiation have been considerably higher in the BIT group than in the BI group. Nonetheless, the mRNA expression levels of downregulated hub genes involved in adipogenic differentiation were drastically lower inside the BIT group thanFrontiers in Genetics | frontiersin.orgNovember 2021 | Volume 12 | ArticleDu et al.Key Genes of Osteogenic and Adipogenic DifferentiationFIGURE three | Gene Ontology (GO) functional enrichment of differentially expressed genes (DEGs) in osteogenic and adipogenic differentiation of human bone marrow mesenchymal stem cells (hMSCs). These genes were enriched in numerous biological procedure (BP), cellular component (CC), and molecular function (MF) terms. The ordinate is indicated on a -log10 (p-value) scale. (A) The key enrichment PI3Kγ web results with the upregulated genes. (B) The key enrichment αvβ6 Storage & Stability outcomes from the downregulated genes.TABLE two | KEGG pathways enrichment analyses of upregulated DEGs. Category KEGG_PATHWAY KEGG_PATHWAY KEGG_PATHWAY Term hsa04550: Signaling pathways regulating pluripotency of stem cells hsa04390: Hippo signaling pathway hsa04960: Aldosterone-regulated sodium reabsorpti