Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30186872", "kind": "science-record", "revision": 8, "content_hash": "sha256:557a3cb4e954f7dc17811cffc9cae08f391b5fae276a0bb1d403a5cb9a6d8d43", "created_at": "2026-11-01T15:40:37Z", "updated_at": "2026-11-01T22:43:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis.", "doi": "10.1155/2018/9482726", "pmid": "30186872", "authors": ["Zhaoyan Li", "Qingyu Wang", "Gaoyang Chen", "Xin Li", "Qiwei Yang", "Zhenwu Du", "Ming Ren", "Yang Song", "Guizhen Zhang"], "journal": "BioMed research international", "year": 2018, "abstract": "Osteoarthritis (OA) is one of the most common diseases worldwide, but the pathogenic genes and pathways are largely unclear. The aim of this study was to screen and verify hub genes involved in OA and explore potential molecular mechanisms. The expression profiles of GSE12021 and GSE55235 were downloaded from the Gene Expression Omnibus (GEO) database, which contained 39 samples, including 20 osteoarthritis synovial membranes and 19 matched normal synovial membranes. The raw data were integrated to obtain differentially expressed genes (DEGs) and were deeply analyzed by bioinformatics methods. The Gene Ontology (GO) and pathway enrichment of DEGs were performed by DAVID and Kyoto Encyclopedia of Genes and Genomes (KEGG) online analyses, respectively. The protein-protein interaction (PPI) networks of the DEGs were constructed based on data from the STRING database. The top 10 hub genes VEGFA, IL6, JUN, IL1β, MYC, IL4, PTGS2, ATF3, EGR1, and DUSP1 were identified from the PPI network. Module analysis revealed that OA was associated with significant pathways including TNF signaling pathway, cytokine-cytokine receptor interaction, and osteoclast differentiation. The qRT-PCR result showed that the expression level of IL6, VEGFA, JUN, IL-1β, and ATF3 was significantly increased in OA samples (p < 0.05), and these candidate genes could be used as potential diagnostic biomarkers and therapeutic targets of OA.", "claims": [{"id": "claim-method", "statement": "The raw data were preprocessed by affy package [8] in R software and limma package [9] in R software was used to identify the upregulated and downregulated DEGs between osteoarthritis synovial membranes and normal controls. P values were adjusted using the Benjamini and Hochberg test, and p < 0.05 and |log⁡FC| > 1 were considered as the cutoff criterion.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30186872", "locator": "sections[4] \"2.2. Data Processing and Identification of DEGs\" paragraph 2", "quote": "The raw data were preprocessed by affy package [8] in R software and limma package [9] in R software was used to identify the upregulated and downregulated DEGs between osteoarthritis synovial membranes and normal controls. P values were adjusted using the Benjamini and Hochberg test, and p < 0.05 and |log⁡FC| > 1 were considered as the cutoff criterion."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30186872", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "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:30186872"], "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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