Bioinformatics Analysis and Identification of Genes and Molecular Pathways Involved in Synovial Inflammation in Rheumatoid Arthritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30916045", "kind": "science-record", "revision": 5, "content_hash": "sha256:dc6caa11ddf15730d7947d7279a2f0c3703fe5f1fa406e7d012fc091c7bebdaa", "created_at": "2026-11-01T15:40:43Z", "updated_at": "2026-11-01T22:00:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis and Identification of Genes and Molecular Pathways Involved in Synovial Inflammation in Rheumatoid Arthritis.", "doi": "10.12659/MSM.915451", "pmid": "30916045", "authors": ["Yuan Xiong", "Bo-Bin Mi", "Meng-Fei Liu", "Hang Xue", "Qi-Peng Wu", "Guo-Hui Liu"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2019, "abstract": "BACKGROUND Rheumatoid arthritis (RA) has a high prevalence in the elderly population. The genes and pathways in the inflamed synovium in patients with RA are poorly understood. This study aimed to identify differentially expressed genes (DEGs) linked to the progression of synovial inflammation in RA using bioinformatics analysis. MATERIAL AND METHODS Gene expression profiles of datasets GSE55235 and GSE55457 were acquired from the Gene Expression Omnibus (GEO) database. DEGs were identified using Morpheus software, and co-expressed DEGs were identified with Venn diagrams. Protein-protein interaction (PPI) networks were assembled with Cytoscape software and separated into subnetworks using the Molecular Complex Detection (MCODE) algorithm. The functions of the top module were assessed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. RESULTS DEGs that were upregulated were significantly enhanced in protein binding, the cell cytosol, organization of the extracellular matrix (ECM), regulation of RNA transcription, and cell adhesion. DEGs that were downregulated were associated with control of the immune response, B-cell and T-cell receptor signaling pathway regulation. KEGG pathway analysis showed that upregulated DEGs enhanced pathways associated with the cell adherens junction, osteoclast differentiation, and hereditary cardiomyopathies. Downregulated DEGs were enriched in primary immunodeficiency, cell adhesion molecules (CAMs), cytokine-cytokine receptor interaction, and hematopoietic cell lineages. CONCLUSIONS The findings from this bioinformatics network analysis study identified molecular mechanisms and the key hub genes that may contribute to synovial inflammation in patients with RA.", "claims": [{"id": "claim-method", "statement": "To determine the DEGs in RA synovium GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE55235) and GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE55457) were used. A DEG was defined by P<0.05 and a fold-change of log2 ≥1. The gene expression profiles, GSE55235 and GSE55457, were acquired from the GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30916045", "locator": "sections[4] \"Identifying differentially expressed genes (DEGs)\" paragraph 2", "quote": "To determine the DEGs in RA synovium GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE55235) and GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE55457) were used."}, {"asset": "source:pmid:30916045", "locator": "sections[4] \"Identifying differentially expressed genes (DEGs)\" paragraph 2", "quote": "A DEG was defined by P<0.05 and a fold-change of log2 ≥1."}, {"asset": "source:pmid:30916045", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "The gene expression profiles, GSE55235 and GSE55457, were acquired from the GEO database."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data from ten samples of synovium from normal individuals (GSM1332201, GSM1332202, GSM1332203, GSM1332204, GSM1332205, GSM1332206, GSM1332207, GSM1332208, GSM1332209, and GSM1332210), and synovium from ten patients with RA (GSM1332221, GSM1332222, GSM1332223, GSM1332224, GSM1332225, GSM1332226, GSM1332227, GSM1332228, GSM1332229, and GSM1332230) were obtained from the GSE55235 dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30916045", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "Data from ten samples of synovium from normal individuals (GSM1332201, GSM1332202, GSM1332203, GSM1332204, GSM1332205, GSM1332206, GSM1332207, GSM1332208, GSM1332209, and GSM1332210), and synovium from ten patients with RA (GSM1332221, GSM1332222, GSM1332223, GSM1332224, GSM1332225, GSM1332226, GSM1332227, GSM1332228, GSM1332229, and GSM1332230) were obtained from the GSE55235 dataset."}], "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:30916045"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE55235"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE55235"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30916045", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.915451", "sha256": 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