Analysis of protein-protein interaction network and functional modules on primary osteoporosis

European Journal of Medical Research

Yong-He Hu¹  Tao Deng¹  Jian Rong¹  Shu-Rong Bai¹  Yang Qin¹  Yi-Min Yao²  Bing-Ang Wang²  Xian-Hua Xu¹  Gai-Li Li¹ 

[1] Department of Geriatrics, Chengdu Military General Hospital, No. 270, Rongdu Avenue, Jinniu District, Chengdu 610083, China;Department of Orthopedics, 452 Hospital of the People’s Liberation Army, Shunjiang Road, Chengdu 610021, China

关键词: Topological properties;    Differentially expressed genes;    Functional modules;    Protein-protein interaction network;    Primary osteoporosis;   

Others  :  817517
DOI  :  10.1186/2047-783X-19-15

 received in 2013-09-06, accepted in 2014-02-19,  发布年份 2014

【 摘 要 】

Background

Primary osteoporosis is an age-related disease, and the main cause of this disease is the failure of bone homeostasis. Previous studies have shown that primary osteoporosis is associated with gene mutations.

To explore the functional modules of the PPI (protein-protein interaction) network of differentially expressed genes (DEGs), and the related pathways participating in primary osteoporosis.

Methods

The gene expression profile of primary osteoporosis GSE35956 was downloaded from the GEO (Gene Expression Omnibus) database and included five MSC (mesenchymal stem cell) specimens of normal osseous tissue and five MSC specimens of osteoporosis. The DEGs between the two types of MSC specimens were identified by the samr package in R language. In addition, the functions and pathways of DEGs were enriched. Then the DEGs were mapped to String to acquire PPI pairs and the PPI network was constructed with by these PPI pairs. Topological properties of the network were calculated by Network Analyzer, and modules in the network were screened by Cluster ONE software. Subsequently, the fronting five modules whose P-value was less than 1.0e-05 were identified and function analysis was conducted.

Results

A total of 797 genes were filtered as DEGs from these ten specimens of GSE35956 with 660 up-regulated genes and 137 down-regulated genes. Meanwhile, up-regulated DEGs were mainly enriched in functions and pathways related to cell cycle and DNA replication. Furthermore, there were 4,135 PPI pairs and 377 nodes in the PPI network. Four modules were enriched in different pathways, including cell cycle and DNA replication pathway in module 2.

Conclusions

In this paper, we explored the genes and pathways involved in primary osteoporosis based on gene expression profiles, and the present findings have the potential to be used clinically for the future treatment of primary osteoporosis.

【 授权许可】

   
2014 Li et al.; licensee BioMed Central Ltd.

【 图 表 】

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