mples was virtually on the very same line and close to 0 (Figure 1), indicating superior excellent of standardization. At the 1-day time-point, inside the BIT group, 222 genes have been upregulated in comparison with the BI group, in which 148 genes were downregulated. In the 2-day time-point, inside the BIT group, 328 genes had been upregulated in comparison using the BI group, in which 375 genes have been downregulated. At the 3-day time-point, the corresponding numbers were 533 upregulated and 515 downregulated, and in the 7-day time-point, the corresponding numbers had been 786 upregulated and 754 downregulated. The DEGs in the 4 time-points had been combined, and the overlap of theFrontiers in Genetics | frontiersin.orgNovember 2021 | Volume 12 | ArticleDu et al.Crucial Genes of Osteogenic and Adipogenic DifferentiationFIGURE two | Venn diagrams displaying (A) the 98 upregulated genes and (B) the 66 downregulated genes. A differentially expressed gene (DEG) volcano plot (C) and a heatmap (D) are shown. Red represents upregulated genes, and green represents downregulated genes (p 0.05, logFC 1 or logFC -1).pathways. Although the p-value of “sa05200: Pathways in cancer” was 0.05, it contained a sizable variety of enriched genes.Protein rotein Interaction Networks in the Differentially Expressed Genes and Identification of Hub GenesTo systematically analyze the PPIs of DEGs, PPI networks from the upregulated and downregulated genes were constructed making use of Cytoscape computer SIRT5 Formulation software (Figures 4A,B). Inside the PPI networks in the upregulated genes, the DEGs with the highest connectivity degrees had been BMP2, CTGF, IGF1, TGFB3, MMP13, MMP3, SERPINE1, COMP, ASPN, and IL11. Similarly, inside the PPI networks of upregulated genes, the DEGs with all the highest connectivity degrees were PPARG, TIMP3, ANXA1, ADAMTS5, TIMP4, AGTR1, NQO1, CXCL12, CEBPA, and CFD. The PPI networks from the DEGs from theSTRING database have been deposited into Cytoscape v3.7.2, and after that the cytoHubba plugin from Cytoscape was utilised to determine hub genes of your PPI networks, and hub genes overlapped by MCC, MNC, and Degree. The top seven upregulated hub genes were CTGF, IGF1, BMP2, MMP13, TGFB3, MMP3, and SERPINE1; and the leading seven downregulated hub genes have been PPARG, TIMP3, ANXA1, ADAMTS5, AGTR1, CXCL12, and CEBPA (Figures 4A,B).Hub Gene mRNA TLR8 Compound expression Levels and ValidationmRNA expression levels of upregulated hub genes involved in osteogenic differentiation have been drastically greater inside the BIT group than inside the BI group. However, the mRNA expression levels of downregulated hub genes involved in adipogenic differentiation were significantly lower within the BIT group thanFrontiers in Genetics | frontiersin.orgNovember 2021 | Volume 12 | ArticleDu et al.Essential 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 had been enriched in various biological process (BP), cellular component (CC), and molecular function (MF) terms. The ordinate is indicated on a -log10 (p-value) scale. (A) The main enrichment results in the upregulated genes. (B) The primary enrichment benefits 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
