The Identified Hub Gene GlcN in Osteoarthritis Progression and Treatment.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34754325", "kind": "science-record", "revision": 4, "content_hash": "sha256:a15a246c73ad4b0c53af1cb313b3ddca9899e0485b64035a1ee41ecb136287d5", "created_at": "2026-11-01T17:36:26Z", "updated_at": "2026-11-01T22:05:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Identified Hub Gene GlcN in Osteoarthritis Progression and Treatment.", "doi": "10.1155/2021/5499450", "pmid": "34754325", "authors": ["Jingsheng Liu", "Xiaoli Dong", "Yining Liu", "Kai Wang", "Shuanhu Lei", "Mingxuan Yang", "Haiyuan Yue", "Haijun Feng", "Kai Feng", "Kang Li", "Jianwei Zhou", "Yanqiang Chen", "Wenjia Du", "Xuewen Kang", "Yayi Xia"], "journal": "Computational and mathematical methods in medicine", "year": 2021, "abstract": "BACKGROUND: As a chronic disease, osteoarthritis has caused great trouble to the health of middle-aged and elderly people. Studies have shown that glucosamine (GlcN) can be used to abate the progression and improve this disease. Based on this point of view, we try to verify the connection between GlcN and osteoarthritis and find more effective biomarkers.\nMETHODS: We downloaded the GSE72575 data set from the GEO database, and used the R language to perform DEG analysis on the gene expression profile of the samples. Next, the GO function and the KEGG signaling pathways were analyzed through the DAVID database, and then, the KEGG pathways enriched in the gene set were analyzed based on GSEA. Then, the PPI network of DEGs was constructed based on the STRING online database, and finally, the hub genes were selected by Cytoscape.\nRESULTS: Three GlcN-treated MH7A cell treatment groups and 3 control groups in the GSE72575 data set were studied. Through analysis, there were 52 DEGs in these samples. Then, through GO, KEGG, and GSEA, regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway, FoxO signaling pathway, JAK-STAT signaling pathway, PI3K-Akt signaling pathway, TGF-beta signaling pathway, and ECM receptor interaction were involved in the regulatory mechanisms of the osteoarthritis pathogenesis. After that, the hub genes IL6 and DDIT3 were identified through PPI network construction and analysis. And it was found that IL6 was lowly expressed in the group with GlcN-treated MH7A cells, while DDIT3 was highly expressed.\nCONCLUSION: The above results provide a basis for GlcN to participate in the treatment of osteoarthritis and a possibility for finding effective therapeutic targets.", "claims": [{"id": "claim-method", "statement": "The data in GSE72575 were preprocessed, and probe annotations were carried out through R language. P < 0.05 was used as the screening condition for DEGs, and the final results were expressed in the form of heat maps.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34754325", "locator": "sections[4] \"2.2. Data Preprocessing and DEG Screening\" paragraph 2", "quote": "The data in GSE72575 were preprocessed, and probe annotations were carried out through R language. P < 0.05 was used as the screening condition for DEGs, and the final results were expressed in the form of heat maps."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data sets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34754325", "locator": "sections[15] \"Data Availability\" paragraph 2", "quote": "The data sets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Through analysis, there were 52 DEGs in these samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34754325", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Through analysis, there were 52 DEGs in these samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Through analysis, there were 52 DEGs in these samples.", "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:34754325"], "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:GSE72575"], "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:GSE72575"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34754325", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/5499450", "sha256": "sha256:6c5e7eb482a2f77788aca86207fa6413845123bd64b3cb57f3f6aa8678ff7a9e", "bytes": 24301, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/5499450", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8572607", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE72575", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72575", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE72575", "version": null, "note": "The data sets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data sets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1865425", "GSM1865426", "GSM1865427", "GSM1865428", "GSM1865429", "GSM1865430", "GSM1865431", "GSM1865432", "GSM1865433", "GSM1865434", "GSM1865435", "GSM1865436", "GSM1865437", "GSM1865438", "GSM1865439"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Expression data from glucosamine-treated human synovial MH7A cells", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE72575 not downloaded", "asset:data:geo:GSE72575 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-2", "family": null, "specific": null, "label": "DEG analysis using R language with P < 0.05 screening", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The data in GSE72575 were preprocessed, and probe annotations were carried out through R language. 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