Identification of key candidate genes and pathways in rheumatoid arthritis and osteoarthritis by integrated bioinformatical analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36861127", "kind": "science-record", "revision": 3, "content_hash": "sha256:d4b4fd316f5c18e268ad0891020436f5a730fac61d6f0cc1db3a30f58ad769c1", "created_at": "2026-11-01T19:01:29Z", "updated_at": "2026-11-01T22:08:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key candidate genes and pathways in rheumatoid arthritis and osteoarthritis by integrated bioinformatical analysis.", "doi": "10.3389/fgene.2023.1083615", "pmid": "36861127", "authors": ["Huijing Huang", "Xinyi Dong", "Kaimin Mao", "Wanwan Pan", "Bin'en Nie", "Lindi Jiang"], "journal": "Frontiers in genetics", "year": 2023, "abstract": "Rheumatoid arthritis (RA) and osteoarthritis (OA) are the most common joint disorders. Although they have shown analogous clinical manifestations, the pathogenesis of RA and OA are different. In this study, we used the online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE153015 to identify gene signatures between RA and OA joints. The relevant data on 8 subjects obtained from large joints of RA patients (RA-LJ), 8 subjects obtained from small joints of RA patients (RA-SJ), and 4 subjects with OA were investigated. Differentially expressed genes (DEGs) were screened. Functional enrichment analysis of DEGs including the Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, which were mainly associated with T cell activation or chemokine activity. Besides, protein-protein interaction (PPI) network analysis was performed, and key modules were identified. Hub genes of RA-LJ and OA groups were screened, they were CD8A, GZMB, CCL5, CD2, and CXCL9, whereas CD8A, CD2, IL7R, CD27, and GZMB were hub genes of RA-SJ and OA group. The novel DEGs and functional pathways between RA and OA identified in this study may provide new insight into the underlying molecular mechanisms and therapeutic strategies of RA and OA.", "claims": [{"id": "claim-method", "statement": "To screen for DEGs, we compared expression profiles of large and small joints of RA patients and OA patients using the online analysis tool GEO2R. p-values and adjusted p-values were calculated via t-tests and statistically significant DEGs were defined with the criteria of 1) a |log2 (fold-change)| >1 and 2) an adjusted p < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36861127", "locator": "sections[4] \"Differential expression analysis\" paragraph 2", "quote": "To screen for DEGs, we compared expression profiles of large and small joints of RA patients and OA patients using the online analysis tool GEO2R. p-values and adjusted p-values were calculated via t-tests and statistically significant DEGs were defined with the criteria of 1) a |log2 (fold-change)| >1 and 2) an adjusted p < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number (s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36861127", "locator": "sections[16] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number (s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differential-expression and protein-protein-interaction analyses identified hub genes distinguishing RA large and small joints from OA joints, and immunohistochemistry validated higher expression of the seven hub genes in RA joints.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36861127", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Hub genes of RA-LJ and OA groups were screened, they were CD8A, GZMB, CCL5, CD2, and CXCL9, whereas CD8A, CD2, IL7R, CD27, and GZMB were hub genes of RA-SJ and OA group."}, {"asset": "source:pmid:36861127", "locator": "sections[12] \"PPI network analysis of DEGs\" paragraph 4", "quote": "In RA joints, CD8A, CD2, GZMB, CCL5, CXCL9, IL7R, and CD27 levels were significantly higher than in OA joints."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differential-expression and protein-protein-interaction analyses identified hub genes distinguishing RA large and small joints from OA joints, and immunohistochemistry validated higher expression of the seven hub genes in RA joints.", "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:36861127"], "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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