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Microarray analysis of genes and gene functions in disc degeneration

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...

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Autores principales: TANG, YANCHUN, WANG, SHAOKUN, LIU, YING, WANG, XUYUN
Formato: Online Artículo Texto
Lenguaje:English
Publicado: D.A. Spandidos 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3881058/
https://www.ncbi.nlm.nih.gov/pubmed/24396401
http://dx.doi.org/10.3892/etm.2013.1421
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author TANG, YANCHUN
WANG, SHAOKUN
LIU, YING
WANG, XUYUN
author_facet TANG, YANCHUN
WANG, SHAOKUN
LIU, YING
WANG, XUYUN
author_sort TANG, YANCHUN
collection PubMed
description 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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spelling pubmed-38810582014-01-06 Microarray analysis of genes and gene functions in disc degeneration TANG, YANCHUN WANG, SHAOKUN LIU, YING WANG, XUYUN Exp Ther Med Articles 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. D.A. Spandidos 2014-02 2013-11-22 /pmc/articles/PMC3881058/ /pubmed/24396401 http://dx.doi.org/10.3892/etm.2013.1421 Text en Copyright © 2014, Spandidos Publications http://creativecommons.org/licenses/by/3.0 This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
spellingShingle Articles
TANG, YANCHUN
WANG, SHAOKUN
LIU, YING
WANG, XUYUN
Microarray analysis of genes and gene functions in disc degeneration
title Microarray analysis of genes and gene functions in disc degeneration
title_full Microarray analysis of genes and gene functions in disc degeneration
title_fullStr Microarray analysis of genes and gene functions in disc degeneration
title_full_unstemmed Microarray analysis of genes and gene functions in disc degeneration
title_short Microarray analysis of genes and gene functions in disc degeneration
title_sort microarray analysis of genes and gene functions in disc degeneration
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3881058/
https://www.ncbi.nlm.nih.gov/pubmed/24396401
http://dx.doi.org/10.3892/etm.2013.1421
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