Differences in key genes in human alveolar macrophages between phenotypically normal smokers and nonsmokers: diagnostic and prognostic value in lung cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33284895", "kind": "science-record", "revision": 4, "content_hash": "sha256:1ac21e32c1f918a8f7f76784627926977866fdc5d31d3b09b408720048709286", "created_at": "2026-11-01T17:34:26Z", "updated_at": "2026-11-01T22:02:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "partial", "title": "Differences in key genes in human alveolar macrophages between phenotypically normal smokers and nonsmokers: diagnostic and prognostic value in lung cancer.", "doi": null, "pmid": "33284895", "authors": ["Yi-De Wang", "Zheng Li", "Feng-Sen Li"], "journal": "International journal of clinical and experimental pathology", "year": 2020, "abstract": "OBJECTIVE: To explore the effect of smoking on gene expression in human alveolar macrophages and the value of identified key genes in the early diagnosis and prognosis of lung cancers.\nMETHODS: We downloaded three data sets (GSE8823, GSE2125, and GSE3212) from the Gene Expression Omnibus (GEO) database, including 31 non-smoking and 33 smoking human alveolar macrophage samples. We identified common differentially expressed genes (DEGs), from which we obtained module genes and hub genes by using STRING and Cytoscape. Then we analyzed the protein-protein interaction (PPI) network of DEGs, hub genes, and module genes and used David online analysis tool to carry out functional enrichment analysis of DEGs and module genes.\nRESULTS: A total of 85 differentially expressed genes was obtained, including 42 up-regulated genes and 43 down-regulated genes. The Human Protein Atlas and Survival analysis showed that GBP1, ITGAM, CSF1, SPP1, COL1A1, LAMB1 and THBS1 may be closely associated with the carcinogenesis and prognosis of lung cancer.\nCONCLUSION: DEGs, module, and hub genes identified in the present study help explain the effects of smoking on human alveolar macrophages and provide candidate targets for diagnosis and treatment of smoking-related lung cancer.", "claims": [{"id": "claim-data-access", "statement": "We downloaded three data sets (GSE8823, GSE2125, and GSE3212) from the Gene Expression Omnibus (GEO) database, including 31 non-smoking and 33 smoking human alveolar macrophage samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33284895", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We downloaded three data sets (GSE8823, GSE2125, and GSE3212) from the Gene Expression Omnibus (GEO) database, including 31 non-smoking and 33 smoking human alveolar macrophage samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 85 differentially expressed genes was obtained, including 42 up-regulated genes and 43 down-regulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:33284895", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 85 differentially expressed genes was obtained, including 42 up-regulated genes and 43 down-regulated genes."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "complete", "objective": "A total of 85 differentially expressed genes was obtained, including 42 up-regulated genes and 43 down-regulated genes.", "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:33284895"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE2125"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE2125"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33284895", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": null, "sha256": "sha256:01ccd3fe2d184bcb2a7239b7ead0b33f61431cf4cbdc03808b8fabb18afaeca6", "bytes": 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three data sets (GSE8823, GSE2125, and GSE3212) from the Gene Expression Omnibus (GEO) database, including 31 non-smoking and 33 smoking human alveolar macrophage samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded three data sets (GSE8823, GSE2125, and GSE3212) from the Gene Expression Omnibus (GEO) database, including 31 non-smoking and 33 smoking human alveolar macrophage samples.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM219241", "GSM219242", "GSM219243", "GSM219244", "GSM219245", "GSM219246", "GSM219247", "GSM219248", "GSM219249", "GSM219250", "GSM219251", "GSM219252", "GSM219253", "GSM219254", "GSM219255", "GSM219256", "GSM219257", "GSM219258", "GSM219259", "GSM219260", "GSM219261", "GSM219262", "GSM219263", "GSM219264"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Overexpression of the 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