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Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis

Osteoarthritis (OA) is one of the most common diseases worldwide, but the pathogenic genes and pathways are largely unclear. The aim of this study was to screen and verify hub genes involved in OA and explore potential molecular mechanisms. The expression profiles of GSE12021 and GSE55235 were downl...

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Autores principales: Li, Zhaoyan, Wang, Qingyu, Chen, Gaoyang, Li, Xin, Yang, Qiwei, Du, Zhenwu, Ren, Ming, Song, Yang, Zhang, Guizhen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6112076/
https://www.ncbi.nlm.nih.gov/pubmed/30186872
http://dx.doi.org/10.1155/2018/9482726
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author Li, Zhaoyan
Wang, Qingyu
Chen, Gaoyang
Li, Xin
Yang, Qiwei
Du, Zhenwu
Ren, Ming
Song, Yang
Zhang, Guizhen
author_facet Li, Zhaoyan
Wang, Qingyu
Chen, Gaoyang
Li, Xin
Yang, Qiwei
Du, Zhenwu
Ren, Ming
Song, Yang
Zhang, Guizhen
author_sort Li, Zhaoyan
collection PubMed
description Osteoarthritis (OA) is one of the most common diseases worldwide, but the pathogenic genes and pathways are largely unclear. The aim of this study was to screen and verify hub genes involved in OA and explore potential molecular mechanisms. The expression profiles of GSE12021 and GSE55235 were downloaded from the Gene Expression Omnibus (GEO) database, which contained 39 samples, including 20 osteoarthritis synovial membranes and 19 matched normal synovial membranes. The raw data were integrated to obtain differentially expressed genes (DEGs) and were deeply analyzed by bioinformatics methods. The Gene Ontology (GO) and pathway enrichment of DEGs were performed by DAVID and Kyoto Encyclopedia of Genes and Genomes (KEGG) online analyses, respectively. The protein-protein interaction (PPI) networks of the DEGs were constructed based on data from the STRING database. The top 10 hub genes VEGFA, IL6, JUN, IL1β, MYC, IL4, PTGS2, ATF3, EGR1, and DUSP1 were identified from the PPI network. Module analysis revealed that OA was associated with significant pathways including TNF signaling pathway, cytokine-cytokine receptor interaction, and osteoclast differentiation. The qRT-PCR result showed that the expression level of IL6, VEGFA, JUN, IL-1β, and ATF3 was significantly increased in OA samples (p < 0.05), and these candidate genes could be used as potential diagnostic biomarkers and therapeutic targets of OA.
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spelling pubmed-61120762018-09-05 Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis Li, Zhaoyan Wang, Qingyu Chen, Gaoyang Li, Xin Yang, Qiwei Du, Zhenwu Ren, Ming Song, Yang Zhang, Guizhen Biomed Res Int Research Article Osteoarthritis (OA) is one of the most common diseases worldwide, but the pathogenic genes and pathways are largely unclear. The aim of this study was to screen and verify hub genes involved in OA and explore potential molecular mechanisms. The expression profiles of GSE12021 and GSE55235 were downloaded from the Gene Expression Omnibus (GEO) database, which contained 39 samples, including 20 osteoarthritis synovial membranes and 19 matched normal synovial membranes. The raw data were integrated to obtain differentially expressed genes (DEGs) and were deeply analyzed by bioinformatics methods. The Gene Ontology (GO) and pathway enrichment of DEGs were performed by DAVID and Kyoto Encyclopedia of Genes and Genomes (KEGG) online analyses, respectively. The protein-protein interaction (PPI) networks of the DEGs were constructed based on data from the STRING database. The top 10 hub genes VEGFA, IL6, JUN, IL1β, MYC, IL4, PTGS2, ATF3, EGR1, and DUSP1 were identified from the PPI network. Module analysis revealed that OA was associated with significant pathways including TNF signaling pathway, cytokine-cytokine receptor interaction, and osteoclast differentiation. The qRT-PCR result showed that the expression level of IL6, VEGFA, JUN, IL-1β, and ATF3 was significantly increased in OA samples (p < 0.05), and these candidate genes could be used as potential diagnostic biomarkers and therapeutic targets of OA. Hindawi 2018-08-14 /pmc/articles/PMC6112076/ /pubmed/30186872 http://dx.doi.org/10.1155/2018/9482726 Text en Copyright © 2018 Zhaoyan Li et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Li, Zhaoyan
Wang, Qingyu
Chen, Gaoyang
Li, Xin
Yang, Qiwei
Du, Zhenwu
Ren, Ming
Song, Yang
Zhang, Guizhen
Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis
title Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis
title_full Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis
title_fullStr Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis
title_full_unstemmed Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis
title_short Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis
title_sort integration of gene expression profile data to screen and verify hub genes involved in osteoarthritis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6112076/
https://www.ncbi.nlm.nih.gov/pubmed/30186872
http://dx.doi.org/10.1155/2018/9482726
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