Microarray analysis of genes and gene functions in disc degeneration

Tang,Yanchun; Wang,Shaokun; Liu,Ying; Wang,Xuyun

doi:10.3892/etm.2013.1421

Microarray analysis of genes and gene functions in disc degeneration

Authors:
- Yanchun Tang
- Shaokun Wang
- Ying Liu
- Xuyun Wang
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Affiliations: Department of Rheumatism and Immunity, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China, Department of Health, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
Published online on: November 22, 2013 https://doi.org/10.3892/etm.2013.1421
Pages: 343-348

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Abstract

The aim of the present study was to screen differentially expressed genes (DEGs) in human degenerative intervertebral discs (IVDs), and to perform functional analysis on these DEGs. The gene expression profile was downloaded from the Gene Expression Omnibus database (GSE34095)and included six human IVD samples: three degenerative and three non‑degenerative. The DEGs between the normal and disease samples were identified using R packages. The online software WebGestalt was used to perform the functional analysis of the DEGs, followed by Osprey software to search for interactions between the DEGs. The Database for Annotation, Visualization and Integrated Discovery was utilized to annotate the DEGs in the interaction network and then the DEGs were uploaded to the Connectivity Map database to search for small molecules. In addition, the active binding sites for the hub genes in the network were obtained, based on the Universal Protein database. By comparing the gene expression profiles of the non‑degenerative and degenerative IVDs, the DEGs between the samples were identified. The DEGs were significantly associated with transforming growth factor β and the extracellular matrix. Matrix metalloproteinase 2 (MMP2) was identified as the hub gene of the interaction network of DEGs. In addition, MMP2 was found to be upregulated in degenerative IVDs. The screened small molecules and the active binding sites of MMP2 may facilitate the development of methods to inhibit overexpression of MMP2.

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