Background Like a common metabolic disorder, osteoporosis is characterized by decreasing bone mass density and increased possibility of fragility fracture. signaling pathway and the MAPK signaling pathway were involved in the 5 KEGG pathways. experiments showed that downregulating p53 expression could be potentially protective for osteoporosis. Conclusions Tomatidine can improve osteoporosis, and one of the systems of its actions is attained by modulating p53. Tomatidine may be a promising medication for osteoporosis. experiments. Materials and Strategies Tomatidine-targeted genes prediction The prospective genes of tomatidine had been acquired with Search Device for Interacting Chemical substances (STITCH). STITCH is really a bioinformatic device for prediction and retrieval of relationships among genes, chemicals, and protein. The discussion network of tomatidine and its own focus on genes was determined using the STITCH on-line device [8]. The computation settings had been the following: 3 shells with the utmost number of relationships 10 for every shell; medium self-confidence rating 0.4. The info of tomatidine-targeted genes was brought in into Gephi software program After that, as well as the weighted discussion network was built. Genes enrichment evaluation Cytoscape 3.7.2 was used to create the proteinCprotein discussion (PPI) network [9]. The centrality amount of each gene was acquired. The provided information from the genes was visualized by Circlize [10]. DAVID, (brief for Data source for Annotation, Integrated and Visualization Finding [11,12]) was useful for enrichment evaluation. The symbols of all tomatine-targeted genes had been brought in into DAVID. Enrichment outcomes had been visualized by GOplot [13]. Retrieval from the pathways involved with osteoporosis and computation of distributed pathways MiRWalk can be an on-line bioinformatics atlas device [14]. In this scholarly study, the KEGG pathways involved with osteoporosis had been retrieved with miRWalk. The intersection of tomatidine-targeted genes-related KEGG pathways (values were selected Then. The tomatidine-targeted genes-related area JX 401 of the KEGG pathways was founded using the Pathway Contractor Device 20 (worth 0.05 chosen. There were 110 osteoporosis related KEGG pathways retrieved after searching and calculation in miRWalk. Identification of shared KEGG pathways With Draw Venn Diagram, 39 shared KEGG pathways of tomatidine-targeted genes and osteoporosis were identified (Figure 2). As shown in Table 1, the top 5 KEGG pathways were pathway of chronic myeloid leukemia, B cell receptor signaling pathway, pathway in cancer, bladder cancer pathway and progesterone-mediated oocyte maturation pathway. MAPK1, MAP2K1, MAPK3, and RAF1 were involved in all 5 pathways. Therefore, they were considered as the hub genes (Figure 3). The information on CLTB chromosomal positions and connectivity of tomatidine-targeted genes is shown in Figure 4. MAPK1, MAP2K1, MAPK3, JX 401 and RAF1 are located in chr22, chr15, chr16, and chr3, respectively. Open in a separate window Figure 2 Identification of shared KEGG pathways of tomatidine-targeted genes and osteoporosis. There were 110 osteoporosis related KEGG pathways and 76 tomatidine-targeted genes-related KEGG pathways. There were 39 shared KEGG pathways identified with Draw Venn Diagram. Open in a separate window Figure 3 Outcomes of gene enrichment analysis. MAPK1, MAP2K1, MAPK3, and RAF1 were involved in all 5 pathways. The top 3 genes of centrality degree were MAPK1, MAPK3, and FOS. JX 401 hsa05220: pathway of chronic myeloid leukemia, hsa04662: B cell receptor signaling pathway, hsa05200: pathway in cancer, hsa05219: bladder cancer pathway, hsa04914: progesterone-mediated oocyte maturation pathway. Open in a separate window Figure 4 Circular visualization of chromosomal positions and connectivity of tomatidine-targeted genes. The names of the genes are shown in the inner circle. For the heatmap, different colors represent different values of centrality.