Identification of immune-related hub genes in chronic obstructive pulmonary disease
As a prevalent persistent respiratory disease, chronic obstructive pulmonary disease (COPD) is featured by airflow limitation and chronic inflammation. This study focused on the identification of immune-related hub genes in COPD. We employed the GSE38974 dataset to analyze differentially expressed g...
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| Veröffentlicht in: | Journal of the National Medical Association 2024-12, Vol.116 (6), p.673-681 |
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| creator | Zhang, Lingyu Zuo, Liwei |
| description | As a prevalent persistent respiratory disease, chronic obstructive pulmonary disease (COPD) is featured by airflow limitation and chronic inflammation. This study focused on the identification of immune-related hub genes in COPD.
We employed the GSE38974 dataset to analyze differentially expressed genes (DEGs) of COPD. Then, we obtained COPD immune-related DEGs (COPD-IMDEGs) based on the intersection of DEGs and immune-related genes. Subsequently, we carried out Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses on COPD-IMDEGs. We established a protein-protein interaction network based on COPD-IMDEGs. The hub genes were determined by utilizing the Maximal Clique Centrality method. We utilized receiver operating characteristic (ROC) curves to analyze the clinical significance of hub genes in COPD. In addition, potential drugs targeting hub genes were predicted based on interactions between hub gene-corresponding proteins and drugs.
A total of 45 COPD-IMDEGs were obtained through differential analysis. Enrichment analyses showed that COPD-IMDEGs were associated with cytokines, growth factors, and receptor ligands. Ten COPD-IMDEGs were identified as hub genes. As shown by ROC curves, these genes had potential value in identifying COPD patients. Drug prediction results showed that simvastatin and other drugs targeted hub genes.
This study analyzed the potential biological functions enriched by COPD-IMDEGs, identified ten genes as biological markers for diagnosing COPD, and predicted potential drugs for treating COPD. |
| doi_str_mv | 10.1016/j.jnma.2024.10.008 |
| format | Article |
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We employed the GSE38974 dataset to analyze differentially expressed genes (DEGs) of COPD. Then, we obtained COPD immune-related DEGs (COPD-IMDEGs) based on the intersection of DEGs and immune-related genes. Subsequently, we carried out Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses on COPD-IMDEGs. We established a protein-protein interaction network based on COPD-IMDEGs. The hub genes were determined by utilizing the Maximal Clique Centrality method. We utilized receiver operating characteristic (ROC) curves to analyze the clinical significance of hub genes in COPD. In addition, potential drugs targeting hub genes were predicted based on interactions between hub gene-corresponding proteins and drugs.
A total of 45 COPD-IMDEGs were obtained through differential analysis. Enrichment analyses showed that COPD-IMDEGs were associated with cytokines, growth factors, and receptor ligands. Ten COPD-IMDEGs were identified as hub genes. As shown by ROC curves, these genes had potential value in identifying COPD patients. Drug prediction results showed that simvastatin and other drugs targeted hub genes.
This study analyzed the potential biological functions enriched by COPD-IMDEGs, identified ten genes as biological markers for diagnosing COPD, and predicted potential drugs for treating COPD.</description><identifier>ISSN: 0027-9684</identifier><identifier>ISSN: 1943-4693</identifier><identifier>EISSN: 1943-4693</identifier><identifier>DOI: 10.1016/j.jnma.2024.10.008</identifier><identifier>PMID: 39578175</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Chronic obstructive pulmonary disease ; Databases, Genetic ; Enrichment analysis ; Gene Expression Profiling ; Gene Ontology ; Gene Regulatory Networks ; Hub genes ; Humans ; Immunity ; Protein Interaction Maps - genetics ; Protein-drug interactions ; Pulmonary Disease, Chronic Obstructive - genetics ; ROC Curve</subject><ispartof>Journal of the National Medical Association, 2024-12, Vol.116 (6), p.673-681</ispartof><rights>2024 National Medical Association</rights><rights>Copyright © 2024 National Medical Association. Published by Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c1881-a0a9c1a5f19a62fab42d554fddff37d52b304654e46011c7475cca6bfc5de3a03</cites><orcidid>0000-0002-0301-0250</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39578175$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Lingyu</creatorcontrib><creatorcontrib>Zuo, Liwei</creatorcontrib><title>Identification of immune-related hub genes in chronic obstructive pulmonary disease</title><title>Journal of the National Medical Association</title><addtitle>J Natl Med Assoc</addtitle><description>As a prevalent persistent respiratory disease, chronic obstructive pulmonary disease (COPD) is featured by airflow limitation and chronic inflammation. This study focused on the identification of immune-related hub genes in COPD.
We employed the GSE38974 dataset to analyze differentially expressed genes (DEGs) of COPD. Then, we obtained COPD immune-related DEGs (COPD-IMDEGs) based on the intersection of DEGs and immune-related genes. Subsequently, we carried out Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses on COPD-IMDEGs. We established a protein-protein interaction network based on COPD-IMDEGs. The hub genes were determined by utilizing the Maximal Clique Centrality method. We utilized receiver operating characteristic (ROC) curves to analyze the clinical significance of hub genes in COPD. In addition, potential drugs targeting hub genes were predicted based on interactions between hub gene-corresponding proteins and drugs.
A total of 45 COPD-IMDEGs were obtained through differential analysis. Enrichment analyses showed that COPD-IMDEGs were associated with cytokines, growth factors, and receptor ligands. Ten COPD-IMDEGs were identified as hub genes. As shown by ROC curves, these genes had potential value in identifying COPD patients. Drug prediction results showed that simvastatin and other drugs targeted hub genes.
This study analyzed the potential biological functions enriched by COPD-IMDEGs, identified ten genes as biological markers for diagnosing COPD, and predicted potential drugs for treating COPD.</description><subject>Chronic obstructive pulmonary disease</subject><subject>Databases, Genetic</subject><subject>Enrichment analysis</subject><subject>Gene Expression Profiling</subject><subject>Gene Ontology</subject><subject>Gene Regulatory Networks</subject><subject>Hub genes</subject><subject>Humans</subject><subject>Immunity</subject><subject>Protein Interaction Maps - genetics</subject><subject>Protein-drug interactions</subject><subject>Pulmonary Disease, Chronic Obstructive - genetics</subject><subject>ROC Curve</subject><issn>0027-9684</issn><issn>1943-4693</issn><issn>1943-4693</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kE1LAzEQhoMotlb_gAfJ0cvWZJPsB3iR4keh4EE9h2wysSm7SU12C_57t7R69DQwPO_LzIPQNSVzSmhxt5lvfKfmOcn5uJgTUp2gKa05y3hRs1M0JSQvs7qo-ARdpLQhI1ELcY4mrBZlRUsxRW9LA7531mnVu-BxsNh13eAhi9CqHgxeDw3-BA8JO4_1OgbvNA5N6uOge7cDvB3aLngVv7FxCVSCS3RmVZvg6jhn6OPp8X3xkq1en5eLh1WmaVXRTBFVa6qEpbUqcqsanhshuDXGWlYakTeM8EJw4AWhVJe8FFqrorFaGGCKsBm6PfRuY_gaIPWyc0lD2yoPYUiSUZZTTsloZIbyA6pjSCmCldvouvFmSYncy5QbuZcp9zL3u1HVGLo59g9NB-Yv8mtvBO4PAIxf7hxEmbQDr8G4CLqXJrj_-n8AqOyG7A</recordid><startdate>20241201</startdate><enddate>20241201</enddate><creator>Zhang, Lingyu</creator><creator>Zuo, Liwei</creator><general>Elsevier Inc</general><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>7X8</scope><orcidid>https://orcid.org/0000-0002-0301-0250</orcidid></search><sort><creationdate>20241201</creationdate><title>Identification of immune-related hub genes in chronic obstructive pulmonary disease</title><author>Zhang, Lingyu ; Zuo, Liwei</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c1881-a0a9c1a5f19a62fab42d554fddff37d52b304654e46011c7475cca6bfc5de3a03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Chronic obstructive pulmonary disease</topic><topic>Databases, Genetic</topic><topic>Enrichment analysis</topic><topic>Gene Expression Profiling</topic><topic>Gene Ontology</topic><topic>Gene Regulatory Networks</topic><topic>Hub genes</topic><topic>Humans</topic><topic>Immunity</topic><topic>Protein Interaction Maps - genetics</topic><topic>Protein-drug interactions</topic><topic>Pulmonary Disease, Chronic Obstructive - genetics</topic><topic>ROC Curve</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhang, Lingyu</creatorcontrib><creatorcontrib>Zuo, Liwei</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of the National Medical Association</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhang, Lingyu</au><au>Zuo, Liwei</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of immune-related hub genes in chronic obstructive pulmonary disease</atitle><jtitle>Journal of the National Medical Association</jtitle><addtitle>J Natl Med Assoc</addtitle><date>2024-12-01</date><risdate>2024</risdate><volume>116</volume><issue>6</issue><spage>673</spage><epage>681</epage><pages>673-681</pages><issn>0027-9684</issn><issn>1943-4693</issn><eissn>1943-4693</eissn><abstract>As a prevalent persistent respiratory disease, chronic obstructive pulmonary disease (COPD) is featured by airflow limitation and chronic inflammation. This study focused on the identification of immune-related hub genes in COPD.
We employed the GSE38974 dataset to analyze differentially expressed genes (DEGs) of COPD. Then, we obtained COPD immune-related DEGs (COPD-IMDEGs) based on the intersection of DEGs and immune-related genes. Subsequently, we carried out Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses on COPD-IMDEGs. We established a protein-protein interaction network based on COPD-IMDEGs. The hub genes were determined by utilizing the Maximal Clique Centrality method. We utilized receiver operating characteristic (ROC) curves to analyze the clinical significance of hub genes in COPD. In addition, potential drugs targeting hub genes were predicted based on interactions between hub gene-corresponding proteins and drugs.
A total of 45 COPD-IMDEGs were obtained through differential analysis. Enrichment analyses showed that COPD-IMDEGs were associated with cytokines, growth factors, and receptor ligands. Ten COPD-IMDEGs were identified as hub genes. As shown by ROC curves, these genes had potential value in identifying COPD patients. Drug prediction results showed that simvastatin and other drugs targeted hub genes.
This study analyzed the potential biological functions enriched by COPD-IMDEGs, identified ten genes as biological markers for diagnosing COPD, and predicted potential drugs for treating COPD.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>39578175</pmid><doi>10.1016/j.jnma.2024.10.008</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0002-0301-0250</orcidid></addata></record> |
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| ispartof | Journal of the National Medical Association, 2024-12, Vol.116 (6), p.673-681 |
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| subjects | Chronic obstructive pulmonary disease Databases, Genetic Enrichment analysis Gene Expression Profiling Gene Ontology Gene Regulatory Networks Hub genes Humans Immunity Protein Interaction Maps - genetics Protein-drug interactions Pulmonary Disease, Chronic Obstructive - genetics ROC Curve |
| title | Identification of immune-related hub genes in chronic obstructive pulmonary disease |
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