Gene Expression Microarray Data Identify Hub Genes Involved in Osteoarthritis
The present study was performed to explore the underlying molecular mechanisms and screen hub genes of osteoarthritis (OA) via bioinformatics analysis. In total, twenty-five OA synovial tissue samples and 25 normal synovial tissue samples were derived from three datasets, namely, GSE55457, GSE55235,...
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| Format: | Article |
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.870590/full |
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| author | Jian Zhou Dazhi Zou Rongjun Wan Rongjun Wan Jie Liu Qiong Zhou Zhen Zhou Wanchun Wang Cheng Tao Tang Liu |
| author_facet | Jian Zhou Dazhi Zou Rongjun Wan Rongjun Wan Jie Liu Qiong Zhou Zhen Zhou Wanchun Wang Cheng Tao Tang Liu |
| author_sort | Jian Zhou |
| collection | DOAJ |
| description | The present study was performed to explore the underlying molecular mechanisms and screen hub genes of osteoarthritis (OA) via bioinformatics analysis. In total, twenty-five OA synovial tissue samples and 25 normal synovial tissue samples were derived from three datasets, namely, GSE55457, GSE55235, and GSE1919, and were used to identify the differentially expressed genes (DEGs) of OA by R language. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs were conducted using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). A Venn diagram was built to show the potential hub genes identified in all three datasets. The STRING database was used for constructing the protein–protein interaction (PPI) networks and submodules of DEGs. We identified 507 upregulated and 620 downregulated genes. Upregulated DEGs were significantly involved in immune response, MHC class II receptor activity, and presented in the extracellular region, while downregulated DEGs were mainly enriched in response to organic substances, extracellular region parts, and cadmium ion binding. Results of KEGG analysis indicated that the upregulated DEGs mainly existed in cell adhesion molecules (CAMs), while downregulated DEGs were significantly involved in the MAPK signaling pathway. A total of eighteen intersection genes were identified across the three datasets. These include Nell-1, ATF3, RhoB, STC1, and VEGFA. In addition, 10 hub genes including CXCL12, CXCL8, CCL20, and CCL4 were found in the PPI network and module construction. Identification of DEGs and hub genes associated with OA may be helpful for revealing the molecular mechanisms of OA and further promotes the development of relevant biomarkers and drug targets. |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-04-12T14:24:29Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-bc5c1f66de614def8fd2ad8dbdb201542022-12-22T03:29:28ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-06-011310.3389/fgene.2022.870590870590Gene Expression Microarray Data Identify Hub Genes Involved in OsteoarthritisJian Zhou0Dazhi Zou1Rongjun Wan2Rongjun Wan3Jie Liu4Qiong Zhou5Zhen Zhou6Wanchun Wang7Cheng Tao8Tang Liu9Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Spine Surgery, Longhui People’s Hospital, Shaoyang, ChinaBranch of National Clinical Research Center for Respiratory Disease, Department of Respiratory Medicine, National Key Clinical Specialty, Xiangya Hospital, Central South University, Changsha, ChinaNational Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, ChinaDepartment of Cardiology, The Fourth Hospital of Changsha, Changsha, ChinaDepartment of Cardiology, The Fourth Hospital of Changsha, Changsha, ChinaMenzies Institute for Medical Research, University of Tasmania, Hobart, TAS, AustraliaDepartment of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, ChinaThe present study was performed to explore the underlying molecular mechanisms and screen hub genes of osteoarthritis (OA) via bioinformatics analysis. In total, twenty-five OA synovial tissue samples and 25 normal synovial tissue samples were derived from three datasets, namely, GSE55457, GSE55235, and GSE1919, and were used to identify the differentially expressed genes (DEGs) of OA by R language. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs were conducted using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). A Venn diagram was built to show the potential hub genes identified in all three datasets. The STRING database was used for constructing the protein–protein interaction (PPI) networks and submodules of DEGs. We identified 507 upregulated and 620 downregulated genes. Upregulated DEGs were significantly involved in immune response, MHC class II receptor activity, and presented in the extracellular region, while downregulated DEGs were mainly enriched in response to organic substances, extracellular region parts, and cadmium ion binding. Results of KEGG analysis indicated that the upregulated DEGs mainly existed in cell adhesion molecules (CAMs), while downregulated DEGs were significantly involved in the MAPK signaling pathway. A total of eighteen intersection genes were identified across the three datasets. These include Nell-1, ATF3, RhoB, STC1, and VEGFA. In addition, 10 hub genes including CXCL12, CXCL8, CCL20, and CCL4 were found in the PPI network and module construction. Identification of DEGs and hub genes associated with OA may be helpful for revealing the molecular mechanisms of OA and further promotes the development of relevant biomarkers and drug targets.https://www.frontiersin.org/articles/10.3389/fgene.2022.870590/fullosteoarthritisbioinformatics analysisenrichment analysisPPI networkmicroarray |
| spellingShingle | Jian Zhou Dazhi Zou Rongjun Wan Rongjun Wan Jie Liu Qiong Zhou Zhen Zhou Wanchun Wang Cheng Tao Tang Liu Gene Expression Microarray Data Identify Hub Genes Involved in Osteoarthritis Frontiers in Genetics osteoarthritis bioinformatics analysis enrichment analysis PPI network microarray |
| title | Gene Expression Microarray Data Identify Hub Genes Involved in Osteoarthritis |
| title_full | Gene Expression Microarray Data Identify Hub Genes Involved in Osteoarthritis |
| title_fullStr | Gene Expression Microarray Data Identify Hub Genes Involved in Osteoarthritis |
| title_full_unstemmed | Gene Expression Microarray Data Identify Hub Genes Involved in Osteoarthritis |
| title_short | Gene Expression Microarray Data Identify Hub Genes Involved in Osteoarthritis |
| title_sort | gene expression microarray data identify hub genes involved in osteoarthritis |
| topic | osteoarthritis bioinformatics analysis enrichment analysis PPI network microarray |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.870590/full |
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