Bioinformatics analysis of microarray data to identify the candidate biomarkers of lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31333911", "kind": "science-record", "revision": 8, "content_hash": "sha256:49d0416bcefaff212c7da44976ced58380af713d79c4bdda2d796eb329dbbb45", "created_at": "2026-11-01T15:40:47Z", "updated_at": "2026-11-01T22:44:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of microarray data to identify the candidate biomarkers of lung adenocarcinoma.", "doi": "10.7717/peerj.7313", "pmid": "31333911", "authors": ["Tingting Guo", "Hongtao Ma", "Yubai Zhou"], "journal": "PeerJ", "year": 2019, "abstract": "BACKGROUND: Lung adenocarcinoma (LUAD) is the major subtype of lung cancer and the most lethal malignant disease worldwide. However, the molecular mechanisms underlying LUAD are not fully understood.\nMETHODS: Four datasets (GSE118370, GSE85841, GSE43458 and GSE32863) were obtained from the gene expression omnibus (GEO). Identification of differentially expressed genes (DEGs) and functional enrichment analysis were performed using the limma and clusterProfiler packages, respectively. A protein-protein interaction (PPI) network was constructed via Search Tool for the Retrieval of Interacting Genes (STRING) database, and the module analysis was performed by Cytoscape. Then, overall survival analysis was performed using the Kaplan-Meier curve, and prognostic candidate biomarkers were further analyzed using the Oncomine database.\nRESULTS: Totally, 349 DEGs were identified, including 275 downregulated and 74 upregulated genes which were significantly enriched in the biological process of extracellular structure organization, leukocyte migration and response to peptide. The mainly enriched pathways were complement and coagulation cascades, malaria and prion diseases. By extracting key modules from the PPI network, 11 hub genes were screened out. Survival analysis showed that except VSIG4, other hub genes may be involved in the development of LUAD, in which MYH10, METTL7A, FCER1G and TMOD1 have not been reported previously to correlated with LUAD. Briefly, novel hub genes identified in this study will help to deepen our understanding of the molecular mechanisms of LUAD carcinogenesis and progression, and to discover candidate targets for early detection and treatment of LUAD.", "claims": [{"id": "claim-method", "statement": "In the present study, the DEGs between LUAD and normal tissues were identified by limma package (Ritchie et al., 2015). The Benjamini–Hochberg procedure was introduced to reduce the false positive rate (FDR) in multiple comparisons (Benjamini & Hochberg, 1995).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31333911", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "In the present study, the DEGs between LUAD and normal tissues were identified by limma package (Ritchie et al., 2015). The Benjamini–Hochberg procedure was introduced to reduce the false positive rate (FDR) in multiple comparisons (Benjamini & Hochberg, 1995)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:Data is available at NCBI GEO under accession numbers GSE118370, GSE32863, GSE85841 and GSE43458.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31333911", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "The following information was supplied regarding data availability:Data is available at NCBI GEO under accession numbers GSE118370, GSE32863, GSE85841 and GSE43458."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31333911"], "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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