Rhizoma Dioscoreae extract protects against alveolar bone loss by regulating the cell cycle: A predictive study based on the protein‑protein interaction network

Zhang,Zhi‑Guo; Song,Chang‑Heng; Zhang,Fang‑Zhen; Chen,Yan‑Jing; Xiang,Li‑Hua; Xiao,Gary Guishan; Ju,Da‑Hong

doi:10.3892/mmr.2016.5188

Rhizoma Dioscoreae extract protects against alveolar bone loss by regulating the cell cycle: A predictive study based on the protein‑protein interaction network

Authors:
- Zhi‑Guo Zhang
- Chang‑Heng Song
- Fang‑Zhen Zhang
- Yan‑Jing Chen
- Li‑Hua Xiang
- Gary Guishan Xiao
- Da‑Hong Ju
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Affiliations: Institute of Basic Theory, China Academy of Chinese Medical Sciences, Beijing 100700, P.R. China, School of Pharmaceutical Science, Dalian University of Technology, Dalian, Liaoning 116024, P.R. China
Published online on: April 25, 2016 https://doi.org/10.3892/mmr.2016.5188
Pages: 5342-5348

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Abstract

Rhizoma Dioscoreae extract (RDE) exhibits a protective effect on alveolar bone loss in ovariectomized (OVX) rats. The aim of this study was to predict the pathways or targets that are regulated by RDE, by re‑assessing our previously reported data and conducting a protein‑protein interaction (PPI) network analysis. In total, 383 differentially expressed genes (≥3‑fold) between alveolar bone samples from the RDE and OVX group rats were identified, and a PPI network was constructed based on these genes. Furthermore, four molecular clusters (A‑D) in the PPI network with the smallest P‑values were detected by molecular complex detection (MCODE) algorithm. Using Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity Pathway Analysis (IPA) tools, two molecular clusters (A and B) were enriched for biological process in Gene Ontology (GO). Only cluster A was associated with biological pathways in the IPA database. GO and pathway analysis results showed that cluster A, associated with cell cycle regulation, was the most important molecular cluster in the PPI network. In addition, cyclin‑dependent kinase 1 (CDK1) may be a key molecule achieving the cell‑cycle‑regulatory function of cluster A. From the PPI network analysis, it was predicted that delayed cell cycle progression in excessive alveolar bone remodeling via downregulation of CDK1 may be another mechanism underling the anti‑osteopenic effect of RDE on alveolar bone.

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