Identification of key genes and biological pathways in lung adenocarcinoma by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37637684", "kind": "science-record", "revision": 3, "content_hash": "sha256:874ca20c0ef289fe38019c99abf8c7e12c0a091e30eb380be61a114390e85f91", "created_at": "2026-11-01T19:02:25Z", "updated_at": "2026-11-01T22:10:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes and biological pathways in lung adenocarcinoma by integrated bioinformatics analysis.", "doi": "10.12998/wjcc.v11.i23.5504", "pmid": "37637684", "authors": ["Lin Zhang", "Yuan Liu", "Jian-Guo Zhuang", "Jie Guo", "Yan-Tao Li", "Yan Dong", "Gang Song"], "journal": "World journal of clinical cases", "year": 2023, "abstract": "BACKGROUND: The objectives of this study were to identify hub genes and biological pathways involved in lung adenocarcinoma (LUAD) via bioinformatics analysis, and investigate potential therapeutic targets.\nAIM: To determine reliable prognostic biomarkers for early diagnosis and treatment of LUAD.\nMETHODS: To identify potential therapeutic targets for LUAD, two microarray datasets derived from the Gene Expression Omnibus (GEO) database were analyzed, GSE3116959 and GSE118370. Differentially expressed genes (DEGs) in LUAD and normal tissues were identified using the GEO2R tool. The Hiplot database was then used to generate a volcanic map of the DEGs. Weighted gene co-expression network analysis was conducted to cluster the genes in GSE116959 and GSE118370 into different modules, and identify immune genes shared between them. A protein-protein interaction network was established using the Search Tool for the Retrieval of Interacting Genes database, then the CytoNCA and CytoHubba components of Cytoscape software were used to visualize the genes. Hub genes with high scores and co-expression were identified, and the Database for Annotation, Visualization and Integrated Discovery was used to perform enrichment analysis of these genes. The diagnostic and prognostic values of the hub genes were calculated using receiver operating characteristic curves and Kaplan-Meier survival analysis, and gene-set enrichment analysis was conducted. The University of Alabama at Birmingham Cancer data analysis portal was used to analyze relationships between the hub genes and normal specimens, as well as their expression during tumor progression. Lastly, validation of protein expression was conducted on the identified hub genes via the Human Protein Atlas database.\nRESULTS: Three hub genes with high connectivity were identified; cellular retinoic acid binding protein 2 (CRABP2), matrix metallopeptidase 12 (MMP12), and DNA topoisomerase II alpha (TOP2A). High expression of these genes was associated with a poor LUAD prognosis, and the genes exhibited high diagnostic value.\nCONCLUSION: Expression levels of CRABP2, MMP12, and TOP2A in LUAD were higher than those in normal lung tissue. This observation has diagnostic value, and is linked to poor LUAD prognosis. These genes may be biomarkers and therapeutic targets in LUAD, but further research is warranted to investigate their usefulness in these respects.", "claims": [{"id": "claim-method", "statement": "We analyzed DEGs between LUAD and normal tissues in the GSE116959 and GSE118370 datasets using the GEO2R tool", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37637684", "locator": "sections[5] \"Identification of DEGs and data visualization\" paragraph 2", "quote": "We analyzed DEGs between LUAD and normal tissues in the GSE116959 and GSE118370 datasets using the GEO2R tool"}], "state": "complete"}, {"id": "claim-data-access", "statement": "Using the keywords “Lung Adenocarcinoma” and “Homo Sapiens” in our search, we obtained two datasets, GSE116959 (including 57 LUAD tissues and 11 normal tissues) and GSE118370 (including 6 LUAD and 6 normal tissues).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37637684", "locator": "sections[4] \"Microarray data\" paragraph 2", "quote": "Using the keywords “Lung Adenocarcinoma” and “Homo Sapiens” in our search, we obtained two datasets, GSE116959 (including 57 LUAD tissues and 11 normal tissues) and GSE118370 (including 6 LUAD and 6 normal tissues)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "CRABP2, MMP12, and TOP2A had high diagnostic value, were overexpressed in LUAD, and were associated with poor prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37637684", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "High expression of these genes was associated with a poor LUAD prognosis, and the genes exhibited high diagnostic value."}, {"asset": "source:pmid:37637684", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "Expression levels of CRABP2, MMP12, and TOP2A in LUAD were higher than those in normal lung tissue."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "CRABP2, MMP12, and TOP2A had high diagnostic value, were overexpressed in LUAD, and were associated with poor prognosis.", "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:37637684"], "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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