Identification of differential expressed genes common to rheumatoid arthritis and osteoporosis based on GEO database.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41327654", "kind": "science-record", "revision": 4, "content_hash": "sha256:c0d331cebf4e76999d9b05afc7fcedb24b8a335e7eff4fda679c3a27d08818d9", "created_at": "2026-11-01T20:31:21Z", "updated_at": "2026-11-01T22:57:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of differential expressed genes common to rheumatoid arthritis and osteoporosis based on GEO database.", "doi": "10.1097/MD.0000000000045473", "pmid": "41327654", "authors": ["Lei Chen", "Meiduo Li", "Yudan Yao", "Zhengyan Wang", "Zeyu Wang"], "journal": "Medicine", "year": 2025, "abstract": "Rheumatoid arthritis (RA) and osteoporosis (OP) are both immune-mediated inflammatory diseases with similar clinical manifestations. A number of studies have shown that there is some correlation between RA and OP. But the mechanism between RA and OP has not been explored. Therefore, this article aims to explore the hub genes and the differentially expressed genes of RA and OP. We selected GSE55235 and GSE35959 from the Gene Expression Omnibus (GEO) database for the difference analysis. We used the GEO2R in GEO database for screening differentially expressed genes and Metascape for enrichment analysis. The protein-protein interaction network and hub genes were identified using the STRING 11.5 database and Cytoscape (version 3.7.2). Subsequently, build diagnostic models with hub genes. In GSE55235 of RA, we found 1318 genes with differential expression, with 557 genes being up-regulated and 761 genes being down-regulated. In GSE35959 of OP, 2337 differential genes, including 1857 up-regulated and 480 down-regulated genes, were found. Among the 99 differentially expressed genes found in RA and OP, 89 were up-regulated and 10 were down-regulated. Analysis of differentially expressed genes in the protein-protein interaction network by the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes revealed that the enriched genes were associated with immunity. The high correlation score was the basis for selecting 10 hub genes. Such as 1L1R1, SMAD3, FOSL1, and so on. These expression genes showed potential diagnostic value. The differentially expressed genes and hub genes found in this study contribute to the development of novel understandings of the underlying functional mechanisms of RA and OP and the identification of potential therapeutic targets for these conditions.", "claims": [{"id": "claim-method", "statement": "We analyzed the GSE55235 and GSE35959 datasets using the GEO2R online tool in the GEO database, downloaded the data, and used the adjusted P value < .05, | log FC | ≥1.0 standard to organize the data sets. The functionality of GEO2R is based on the “limma” R package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41327654", "locator": "sections[4] \"2.2. Screening for differentially expressed genes\" paragraph 2", "quote": "We analyzed the GSE55235 and GSE35959 datasets using the GEO2R online tool in the GEO database, downloaded the data, and used the adjusted P value < .05, | log FC | ≥1.0 standard to organize the data sets. The functionality of GEO2R is based on the “limma” R package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are publicly available.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41327654", "locator": "sections[18] \"(untitled)\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are publicly available."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Among the 99 differentially expressed genes found in RA and OP, 89 were up-regulated and 10 were down-regulated.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41327654", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Among the 99 differentially expressed genes found in RA and OP, 89 were up-regulated and 10 were down-regulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Among the 99 differentially expressed genes found in RA and OP, 89 were up-regulated and 10 were down-regulated.", "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:41327654"], "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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