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pmid:32771051
Bioinformatics analysis of differentially expressed genes in subchondral bone in early experimental osteoarthritis using microarray data.
Zhao Wang · Yong Ji · Hong-Wei Bao
Journal of orthopaedic surgery and research · 2020 doi:10.1186/s13018-020-01839-8
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Experiment
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Complete file
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The aim of this study is to identify the gene expression profile specific to subchondral bone in OA by comparing the different expression profiles in experimental and sham-operation groups.\nMETHODS: Gene expression profile GSE30322 was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were obtained by limma package. And Database for Annotation, Visualization and Integrated Discovery (DAVID) databases were further used to identify the potential gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, a protein-protein interaction (PPI) network was constructed and significant modules were extracted.\nRESULTS: Totally, 588 DEGs were identified including 199 upregulated DEGs and 389 downregulated DEGs screened in OA and sham-operation. GO showed that DEGs were significantly enhanced for ribosomal subunit export from nucleus and molting cycle. KEGG pathway analysis revealed that target genes were enriched in thiamine metabolism.\nCONCLUSION: These key candidate DEGs that affect the progression of OA, and these genes might serve as potential therapeutic targets for OA.", "claims": [{"id": "claim-method", "statement": "The analysis was carried out using Limma package from Bioconductor project.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32771051", "locator": "sections[4] \"DEGs in E-group and intact S-group samples\" paragraph 2", "quote": "The analysis was carried out using Limma package from Bioconductor project."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data was freely downloaded from the public GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32771051", "locator": "sections[19] \"notes\" paragraph 1", "quote": "The data was freely downloaded from the public GEO database."}], "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:32771051"], "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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