Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes
Background. Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis. Methods. The raw data of GSE89408 were do...
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| description | Background. Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis. Methods. The raw data of GSE89408 were downloaded from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by R software. The DAVID database was used for pathway and gene ontology analysis, and p2 were set as the cut-off point. Moreover, protein-protein interaction (PPI) network construction was applied for exploring the hub genes in osteoarthritis. The expression levels of the top ten hub genes in knee osteoarthritis synovial membranes and controls were detected by quantitative real-time PCR system. Results. A total of 229 DEGs were identified in osteoarthritis synovial membranes compared with normal synovial membranes, including 145 upregulated and 84 downregulated differentially expressed genes. The KEGG pathway analysis results showed that up-DEGs were enriched in proteoglycans in cytokine-cytokine receptor interaction, chemokine signaling pathway, rheumatoid arthritis, and TNF signaling pathway, whereas down-DEGs were enriched in the PPAR signaling pathway and AMPK signaling pathway. The qRT-PCR results showed that the expression levels of ADIPOQ, IL6, and CXCR1 in the synovium of osteoarthritis were significantly increased (p |
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Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis. Methods. The raw data of GSE89408 were downloaded from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by R software. The DAVID database was used for pathway and gene ontology analysis, and p<0.05 and gene count >2 were set as the cut-off point. Moreover, protein-protein interaction (PPI) network construction was applied for exploring the hub genes in osteoarthritis. The expression levels of the top ten hub genes in knee osteoarthritis synovial membranes and controls were detected by quantitative real-time PCR system. Results. A total of 229 DEGs were identified in osteoarthritis synovial membranes compared with normal synovial membranes, including 145 upregulated and 84 downregulated differentially expressed genes. The KEGG pathway analysis results showed that up-DEGs were enriched in proteoglycans in cytokine-cytokine receptor interaction, chemokine signaling pathway, rheumatoid arthritis, and TNF signaling pathway, whereas down-DEGs were enriched in the PPAR signaling pathway and AMPK signaling pathway. The qRT-PCR results showed that the expression levels of ADIPOQ, IL6, and CXCR1 in the synovium of osteoarthritis were significantly increased (p <0.05).</description><identifier>ISSN: 2314-6133</identifier><identifier>EISSN: 2314-6141</identifier><identifier>DOI: 10.1155/2019/8340573</identifier><identifier>PMID: 31139654</identifier><language>eng</language><publisher>Cairo, Egypt: Hindawi Publishing Corporation</publisher><subject>Arthritis ; Biocompatibility ; Chemokines ; Cytokines ; Disease ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Gene Regulatory Networks ; Genes ; Genomics ; Hospitals ; Interleukin 6 ; Joint surgery ; Knee ; Membranes ; Molecular modelling ; Ontology ; Orthopedics ; Osteoarthritis ; Osteoarthritis - genetics ; Pain ; Pathogenesis ; Peroxisome proliferator-activated receptors ; Protein interaction ; Protein Interaction Maps - genetics ; Protein-protein interactions ; Proteins ; Proteoglycans ; Reproducibility of Results ; Rheumatoid arthritis ; Rheumatoid factor ; Signal transduction ; Signal Transduction - genetics ; Signaling ; Software ; Synovium ; Systematic review</subject><ispartof>BioMed research international, 2019-01, Vol.2019 (2019), p.1-9</ispartof><rights>Copyright © 2019 Zhaoyan Li et al.</rights><rights>COPYRIGHT 2019 John Wiley & Sons, Inc.</rights><rights>Copyright © 2019 Zhaoyan Li et al. This is an open access article distributed under the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. https://creativecommons.org/licenses/by/4.0</rights><rights>Copyright © 2019 Zhaoyan Li et al. 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c499t-1bf5d6755e3dea278893bee00e76252dbe39d9fce5cc3b3f9bf9688f782b26ab3</citedby><cites>FETCH-LOGICAL-c499t-1bf5d6755e3dea278893bee00e76252dbe39d9fce5cc3b3f9bf9688f782b26ab3</cites><orcidid>0000-0003-1313-8001 ; 0000-0003-0681-2184 ; 0000-0001-6464-4997 ; 0000-0002-7324-9507 ; 0000-0001-6312-4674</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500622/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500622/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27915,27916,53782,53784</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31139654$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Cucchiarini, Magali</contributor><contributor>Magali Cucchiarini</contributor><creatorcontrib>Zhang, Guizhen</creatorcontrib><creatorcontrib>Song, Yang</creatorcontrib><creatorcontrib>Yang, Qiwei</creatorcontrib><creatorcontrib>Shang, Jing</creatorcontrib><creatorcontrib>Chen, Gaoyang</creatorcontrib><creatorcontrib>Du, Zhenwu</creatorcontrib><creatorcontrib>Zhong, Lei</creatorcontrib><creatorcontrib>Li, Zhaoyan</creatorcontrib><creatorcontrib>Wang, Qingyu</creatorcontrib><title>Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes</title><title>BioMed research international</title><addtitle>Biomed Res Int</addtitle><description>Background. Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis. Methods. The raw data of GSE89408 were downloaded from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by R software. The DAVID database was used for pathway and gene ontology analysis, and p<0.05 and gene count >2 were set as the cut-off point. Moreover, protein-protein interaction (PPI) network construction was applied for exploring the hub genes in osteoarthritis. The expression levels of the top ten hub genes in knee osteoarthritis synovial membranes and controls were detected by quantitative real-time PCR system. Results. A total of 229 DEGs were identified in osteoarthritis synovial membranes compared with normal synovial membranes, including 145 upregulated and 84 downregulated differentially expressed genes. The KEGG pathway analysis results showed that up-DEGs were enriched in proteoglycans in cytokine-cytokine receptor interaction, chemokine signaling pathway, rheumatoid arthritis, and TNF signaling pathway, whereas down-DEGs were enriched in the PPAR signaling pathway and AMPK signaling pathway. The qRT-PCR results showed that the expression levels of ADIPOQ, IL6, and CXCR1 in the synovium of osteoarthritis were significantly increased (p <0.05).</description><subject>Arthritis</subject><subject>Biocompatibility</subject><subject>Chemokines</subject><subject>Cytokines</subject><subject>Disease</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation</subject><subject>Gene Ontology</subject><subject>Gene Regulatory Networks</subject><subject>Genes</subject><subject>Genomics</subject><subject>Hospitals</subject><subject>Interleukin 6</subject><subject>Joint surgery</subject><subject>Knee</subject><subject>Membranes</subject><subject>Molecular modelling</subject><subject>Ontology</subject><subject>Orthopedics</subject><subject>Osteoarthritis</subject><subject>Osteoarthritis - genetics</subject><subject>Pain</subject><subject>Pathogenesis</subject><subject>Peroxisome proliferator-activated receptors</subject><subject>Protein interaction</subject><subject>Protein Interaction Maps - genetics</subject><subject>Protein-protein interactions</subject><subject>Proteins</subject><subject>Proteoglycans</subject><subject>Reproducibility of Results</subject><subject>Rheumatoid arthritis</subject><subject>Rheumatoid factor</subject><subject>Signal transduction</subject><subject>Signal Transduction - genetics</subject><subject>Signaling</subject><subject>Software</subject><subject>Synovium</subject><subject>Systematic review</subject><issn>2314-6133</issn><issn>2314-6141</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>RHX</sourceid><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqN0c1PFDEYBvDGaIQgN8-miRcTWOnHtJ1eTDaIQELkIhcuTTvzli3OTtd2Rtj_3k52XcQTvbRJf3n68SD0npLPlApxwgjVJzWviFD8FdpnnFYzSSv6erfmfA8d5nxPyqipJFq-RXucUq6lqPbR7XcYHmL6iee97dYZMo4efw3eQ4J-CLbr1vjscZUgZ2jxOfRFhB5f5wGiTcMihSFkPER82U7er_HF6DbuHXrjbZfhcDsfoJtvZz9OL2ZX1-eXp_OrWVNpPcyo86KVSgjgLVim6lpzB0AIKMkEax1w3WrfgGga7rjXzmtZ117VzDFpHT9AXza5q9EtoW3KPZLtzCqFpU1rE20wz3f6sDB38beRghDJWAn4tA1I8dcIeTDLkBvoOttDHLMphNZVpZku9ON_9D6OqXzdpKhUlCtdP6k724EJvY_l3GYKNXNJdYFETep4o5oUc07gd1emxEztmqlds2238A__PnOH_3ZZwNEGLELf2ofwwjgoBrx90rR0oAT_A8i0tho</recordid><startdate>20190101</startdate><enddate>20190101</enddate><creator>Zhang, Guizhen</creator><creator>Song, Yang</creator><creator>Yang, Qiwei</creator><creator>Shang, Jing</creator><creator>Chen, Gaoyang</creator><creator>Du, Zhenwu</creator><creator>Zhong, Lei</creator><creator>Li, Zhaoyan</creator><creator>Wang, Qingyu</creator><general>Hindawi Publishing Corporation</general><general>Hindawi</general><general>John Wiley & Sons, Inc</general><general>Hindawi Limited</general><scope>ADJCN</scope><scope>AHFXO</scope><scope>RHU</scope><scope>RHW</scope><scope>RHX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7QO</scope><scope>7T7</scope><scope>7TK</scope><scope>7U7</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>CWDGH</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-1313-8001</orcidid><orcidid>https://orcid.org/0000-0003-0681-2184</orcidid><orcidid>https://orcid.org/0000-0001-6464-4997</orcidid><orcidid>https://orcid.org/0000-0002-7324-9507</orcidid><orcidid>https://orcid.org/0000-0001-6312-4674</orcidid></search><sort><creationdate>20190101</creationdate><title>Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes</title><author>Zhang, Guizhen ; Song, Yang ; Yang, Qiwei ; Shang, Jing ; Chen, Gaoyang ; Du, Zhenwu ; Zhong, Lei ; Li, Zhaoyan ; Wang, Qingyu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c499t-1bf5d6755e3dea278893bee00e76252dbe39d9fce5cc3b3f9bf9688f782b26ab3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Arthritis</topic><topic>Biocompatibility</topic><topic>Chemokines</topic><topic>Cytokines</topic><topic>Disease</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation</topic><topic>Gene Ontology</topic><topic>Gene Regulatory Networks</topic><topic>Genes</topic><topic>Genomics</topic><topic>Hospitals</topic><topic>Interleukin 6</topic><topic>Joint surgery</topic><topic>Knee</topic><topic>Membranes</topic><topic>Molecular modelling</topic><topic>Ontology</topic><topic>Orthopedics</topic><topic>Osteoarthritis</topic><topic>Osteoarthritis - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BioMed research international</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Guizhen</au><au>Song, Yang</au><au>Yang, Qiwei</au><au>Shang, Jing</au><au>Chen, Gaoyang</au><au>Du, Zhenwu</au><au>Zhong, Lei</au><au>Li, Zhaoyan</au><au>Wang, Qingyu</au><au>Cucchiarini, Magali</au><au>Magali Cucchiarini</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes</atitle><jtitle>BioMed research international</jtitle><addtitle>Biomed Res Int</addtitle><date>2019-01-01</date><risdate>2019</risdate><volume>2019</volume><issue>2019</issue><spage>1</spage><epage>9</epage><pages>1-9</pages><issn>2314-6133</issn><eissn>2314-6141</eissn><abstract>Background. Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis. Methods. The raw data of GSE89408 were downloaded from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by R software. The DAVID database was used for pathway and gene ontology analysis, and p<0.05 and gene count >2 were set as the cut-off point. Moreover, protein-protein interaction (PPI) network construction was applied for exploring the hub genes in osteoarthritis. The expression levels of the top ten hub genes in knee osteoarthritis synovial membranes and controls were detected by quantitative real-time PCR system. Results. A total of 229 DEGs were identified in osteoarthritis synovial membranes compared with normal synovial membranes, including 145 upregulated and 84 downregulated differentially expressed genes. The KEGG pathway analysis results showed that up-DEGs were enriched in proteoglycans in cytokine-cytokine receptor interaction, chemokine signaling pathway, rheumatoid arthritis, and TNF signaling pathway, whereas down-DEGs were enriched in the PPAR signaling pathway and AMPK signaling pathway. The qRT-PCR results showed that the expression levels of ADIPOQ, IL6, and CXCR1 in the synovium of osteoarthritis were significantly increased (p <0.05).</abstract><cop>Cairo, Egypt</cop><pub>Hindawi Publishing Corporation</pub><pmid>31139654</pmid><doi>10.1155/2019/8340573</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0003-1313-8001</orcidid><orcidid>https://orcid.org/0000-0003-0681-2184</orcidid><orcidid>https://orcid.org/0000-0001-6464-4997</orcidid><orcidid>https://orcid.org/0000-0002-7324-9507</orcidid><orcidid>https://orcid.org/0000-0001-6312-4674</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Arthritis Biocompatibility Chemokines Cytokines Disease Gene expression Gene Expression Profiling Gene Expression Regulation Gene Ontology Gene Regulatory Networks Genes Genomics Hospitals Interleukin 6 Joint surgery Knee Membranes Molecular modelling Ontology Orthopedics Osteoarthritis Osteoarthritis - genetics Pain Pathogenesis Peroxisome proliferator-activated receptors Protein interaction Protein Interaction Maps - genetics Protein-protein interactions Proteins Proteoglycans Reproducibility of Results Rheumatoid arthritis Rheumatoid factor Signal transduction Signal Transduction - genetics Signaling Software Synovium Systematic review |
| title | Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes |
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