Identifying Crucial Biomarkers in Osteoporosis and Ulcerative Colitis Through Bioinformatics Analysis of Co-expressed Genes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37842511", "kind": "science-record", "revision": 3, "content_hash": "sha256:fa6c99c3ce19265e22b96bbc6e30bca84d059850cfb4557e9a84b1915eb0d9a1", "created_at": "2026-11-01T19:02:42Z", "updated_at": "2026-11-01T22:10:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying Crucial Biomarkers in Osteoporosis and Ulcerative Colitis Through Bioinformatics Analysis of Co-expressed Genes.", "doi": "10.7759/cureus.45063", "pmid": "37842511", "authors": ["Zhengyan Wang", "Xukai Wang", "Jing Yan", "Ying Wang", "Xingxing Yu", "Yanpeng Wang"], "journal": "Cureus", "year": 2023, "abstract": "Osteoporosis (OP) and ulcerative colitis (UC), prevalent immune diseases, exert a substantial socioeconomic impact globally. This study identifies biomarkers for these diseases, paving the way for in-depth research. Initially, the Gene Expression Omnibus (GEO) database was employed to analyze datasets GSE35958 and GSE87466. This analysis aimed to pinpoint co-expression differential genes (DEGs) between OP and UC. Subsequently, the Metascape database facilitated the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEGs' co-expression. For network construction and visualization, the STRING11.5 database along with Cytoscape 3.7.2 (Cytoscape Team, USA) were utilized to create a protein-protein interaction (PPI) network. Moreover, Cytoscape's cytoHubba plugin was instrumental in identifying the central genes, known as hub genes. In the datasets GSE35958 and GSE87466, 156 co-expressed DEGs were discovered. The PPI network, constructed using STRING11.5 and Cytoscape 3.7.2, comprises 96 nodes and 222 connections. Notably, seven hub genes were identified, namely COL6A1, COL6A2, BGN, NID1, PLAU, TGFB1, and PLAUR. These DEGs were predominantly enriched in pathways such as extracellular matrix organization and collagen-containing extracellular matrix, as per GO analysis. For diagnostic model construction and hub gene validation, datasets GSE56815 and GSE107499 from the GEO database were employed. The top five hub genes were validated. In conclusion, the hub genes identified in this study played a significant role in the early diagnosis, prevention, and treatment of OP and UC. Furthermore, they provide fresh insights into the underlying mechanisms of these diseases' development and progression.", "claims": [{"id": "claim-method", "statement": "We used the GSEA database and the Metascape database for GSE35958 and GSE87466 for GSEA enrichment analysis and GO enrichment analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37842511", "locator": "sections[2] \"Materials and methods\" paragraph 9", "quote": "We used the GSEA database and the Metascape database for GSE35958 and GSE87466 for GSEA enrichment analysis and GO enrichment analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We downloaded four datasets from GEO, namely GSE35958, GSE87466, GSE56815, and GSE107499 (Table 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37842511", "locator": "sections[2] \"Materials and methods\" paragraph 6", "quote": "We downloaded four datasets from GEO, namely GSE35958, GSE87466, GSE56815, and GSE107499 (Table 1)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Notably, seven hub genes were identified, namely COL6A1, COL6A2, BGN, NID1, PLAU, TGFB1, and PLAUR.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37842511", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Notably, seven hub genes were identified, namely COL6A1, COL6A2, BGN, NID1, PLAU, TGFB1, and PLAUR."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Notably, seven hub genes were identified, namely COL6A1, COL6A2, BGN, NID1, PLAU, TGFB1, and PLAUR.", "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:37842511"], "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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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE35958", "GSE87466", "GSE56815", "GSE107499"], "resolved_accessions": ["GSE35958", "GSE87466", "GSE56815", "GSE107499"], "statements": ["We downloaded four datasets from GEO, namely GSE35958, GSE87466, GSE56815, and GSE107499 (Table 1)."], "basis": "The paper names GSE35958, GSE87466, GSE56815, GSE107499 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:37842511", "data:geo:GSE107499"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE107499"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:56:13Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 7502, "completion_tokens": 1432, "cached_tokens": 0}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37842511", "type": "paper", "label": "pmid:37842511"}, {"id": "source:pmid:37842511", "type": "manuscript", "label": "PMID 37842511 full text"}, {"id": "data:geo:GSE107499", "type": "dataset", "label": "GEO GSE107499"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37842511", "type": "paper", "label": "pmid:37842511"}, {"id": "source:pmid:37842511", "type": "manuscript", "label": "PMID 37842511 full text"}, {"id": "data:geo:GSE107499", "type": "dataset", "label": "GEO GSE107499"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37842511", "type": "extraction", "used": ["source:pmid:37842511"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE107499", "type": "accession_resolution", "used": ["data:geo:GSE107499"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37842511", "parent_hash": "sha256:d86a4d236148888dd7a17b5b38ba3e42c7ff1f0be683e48a5d19eeb525ae8bd5", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE107499 licence not read", "asset:data:geo:GSE107499 not downloaded", "asset:data:geo:GSE35958 licence not read", "asset:data:geo:GSE35958 not downloaded", "asset:data:geo:GSE56815 licence not read", "asset:data:geo:GSE56815 not downloaded", "asset:data:geo:GSE87466 licence not read", "asset:data:geo:GSE87466 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["le 1). The GPL570 platform ([HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array) serves as", "The GPL13158 platform ([HT_HG-U133_Plus_PM] Affymetrix HT HG-U133+ PM Array Plate) serves as the fo", "for GSE87466. The GPL96 platform ([HG-U133A] Affymetrix Human Genome U133A Array) serves as the foun", "SE56815. The GPL15207 platform, ([PrimeView] Affymetrix Human Gene Expression Array), is the foundat"], "order_basis": "paper_text_order:3231", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}