Identification of Potential Key Genes in the Pathogenesis of Chronic Obstructive Pulmonary Disease Through Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34804123", "kind": "science-record", "revision": 5, "content_hash": "sha256:c475ee650fb0320c19ee71436b4625964ba4ba7235013ee889a5a2cadb4c44aa", "created_at": "2026-11-01T17:36:30Z", "updated_at": "2026-11-01T22:47:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Potential Key Genes in the Pathogenesis of Chronic Obstructive Pulmonary Disease Through Bioinformatics Analysis.", "doi": "10.3389/fgene.2021.754569", "pmid": "34804123", "authors": ["Qingzhou Guan", "Yange Tian", "Zhenzhen Zhang", "Lanxi Zhang", "Peng Zhao", "Jiansheng Li"], "journal": "Frontiers in genetics", "year": 2021, "abstract": "Chronic obstructive pulmonary disease (COPD) is a common respiratory disease with high morbidity and mortality. The etiology of COPD is complex, and the pathogenesis mechanisms remain unclear. In this study, we used rat and human COPD gene expression data from our laboratory and the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs) between individuals with COPD and healthy individuals. Then, protein-protein interaction (PPI) networks were constructed, and hub genes were identified. Cytoscape was used to construct the co-expressed network and competitive endogenous RNA (ceRNA) networks. A total of 198 DEGs were identified, and a PPI network with 144 nodes and 355 edges was constructed. Twelve hub genes were identified by the cytoHubba plugin in Cytoscape. Of these genes, CCR3, CCL2, COL4A2, VWF, IL1RN, IL2RA, and CCL13 were related to inflammation or immunity, or tissue-specific expression in lung tissue, and their messenger RNA (mRNA) levels were validated by qRT-PCR. COL4A2, VWF, and IL1RN were further verified by the GEO dataset GSE76925, and the ceRNA network was constructed with Cytoscape. These three genes were consistent with COPD rat model data compared with control data, and their dysregulation direction was reversed when the COPD rat model was treated with effective-component compatibility of Bufei Yishen formula III. This bioinformatics analysis strategy may be useful for elucidating novel mechanisms underlying COPD. We pinpointed three key genes that may play a role in COPD pathogenesis and therapy, which deserved to be further studied.", "claims": [{"id": "claim-method", "statement": "For the COPD rat data compared with normal controls, edgeR was applied to identify DEGs. For array- and seq-based data from public databases, significance analysis of microarray (SAM) and Wilcoxon rank-sum tests were used to identify DEGs, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34804123", "locator": "sections[3] \"Data Acquisition and Identification of Differentially Expressed Genes\" paragraph 5", "quote": "For the COPD rat data compared with normal controls, edgeR was applied to identify DEGs. For array- and seq-based data from public databases, significance analysis of microarray (SAM) and Wilcoxon rank-sum tests were used to identify DEGs, respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34804123", "locator": "sections[15] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 198 DEGs were identified, and a PPI network with 144 nodes and 355 edges was constructed.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34804123", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 198 DEGs were identified, and a PPI network with 144 nodes and 355 edges was constructed."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A total of 198 DEGs were identified, and a PPI network with 144 nodes and 355 edges was constructed.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34804123"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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In this study, we used rat and human COPD gene expression data from our", "These three genes were consistent with COPD rat model data compared with control data, and t", "ulation direction was reversed when the COPD rat model was treated with effective-component c"], "order_basis": "paper_text_order:303", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["For the COPD rat data compared with normal controls, edgeR was applied to identify DEGs. For array- and seq-based data from public databases, significance analysis of microarray (SAM) and Wilcoxon rank-sum tests were used to identify DEGs, respectively."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}