Integrative meta-analysis of differentially expressed genes in osteoarthritis using microarray technology.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25975828", "kind": "science-record", "revision": 6, "content_hash": "sha256:315498bbef7e38975fd58d63bb145856aab962126831f8dbdadedf6e4e776f7f", "created_at": "2026-11-01T15:40:08Z", "updated_at": "2026-11-01T21:20:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative meta-analysis of differentially expressed genes in osteoarthritis using microarray technology.", "doi": "10.3892/mmr.2015.3790", "pmid": "25975828", "authors": ["Xi Wang", "Yujie Ning", "Xiong Guo"], "journal": "Molecular medicine reports", "year": 2015, "abstract": "The aim of the present study was to identify differentially expressed (DE) genes in patients with osteoarthritis (OA), and biological processes associated with changes in gene expression that occur in this disease. Using the INMEX (integrative meta‑analysis of expression data) software tool, a meta‑analysis of publicly available microarray Gene Expression Omnibus (GEO) datasets of OA was performed. Gene ontology (GO) enrichment analysis was performed in order to detect enriched functional attributes based on gene‑associated GO terms. Three GEO datasets, containing 137 patients with OA and 52 healthy controls, were included in the meta‑analysis. The analysis identified 85 genes that were consistently differentially expressed in OA (30 genes were upregulated and 55 genes were downregulated). The upregulated gene with the lowest P‑value (P=5.36E‑07) was S‑phase kinase‑associated protein 2, E3 ubiquitin protein ligase (SKP2). The downregulated gene with the lowest P‑value (P=4.42E‑09) was Proline rich 5 like (PRR5L). Among the 210 GO terms that were associated with the set of DE genes, the most significant two enrichments were observed in the GO categories of 'Immune response', with a P‑value of 0.000129438, and 'Immune effectors process', with a P‑value of 0.000288619. The current meta‑analysis identified genes that were consistently DE in OA, in addition to biological pathways associated with changes in gene expression that occur during OA, which may provide insight into the molecular mechanisms underlying the pathogenesis of this disease.", "claims": [{"id": "claim-method", "statement": "A random effects model of effect size (ES) measures was used to integrate gene expression patterns.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25975828", "locator": "sections[8] \"Meta-analysis of gene expression in OA\" paragraph 2", "quote": "A random effects model of effect size (ES) measures was used to integrate gene expression patterns."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used INMEX software for a random-effects meta-analysis of publicly available microarray GEO datasets and identified 85 consistently differentially expressed genes in OA, comprising 30 upregulated and 55 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25975828", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Using the INMEX (integrative meta-analysis of expression data) software tool, a meta-analysis of publicly available microarray Gene Expression Omnibus (GEO) datasets of OA was performed."}, {"asset": "source:pmid:25975828", "locator": "sections[8] \"Meta-analysis of gene expression in OA\" paragraph 2", "quote": "A random effects model of effect size (ES) measures was used to integrate gene expression patterns."}, {"asset": "source:pmid:25975828", "locator": "sections[9] \"Identification of differentially expressed genes in OA\" paragraph 2", "quote": "A total of 85 genes were identified, which were consistently differentially expressed in OA. Among these 85 DE genes, 30 were upregulated and 55 were downregulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study used INMEX software for a random-effects meta-analysis of publicly available microarray GEO datasets and identified 85 consistently differentially expressed genes in OA, comprising 30 upregulated and 55 downregulated 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:25975828"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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