Bioinformatic analysis of the molecular mechanisms underlying the progression of bone defects.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37359021", "kind": "science-record", "revision": 3, "content_hash": "sha256:6ab3050bcefc5a84ac0f534193043a5cb0c1c6dd6c16e9aacba3d4b08a053508", "created_at": "2026-11-01T19:02:05Z", "updated_at": "2026-11-01T22:09:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic analysis of the molecular mechanisms underlying the progression of bone defects.", "doi": "10.3389/fmed.2023.1157099", "pmid": "37359021", "authors": ["Hao Liu", "Xuan Zhao", "Yin Li", "Jiang Yi", "Chenxi Zhang", "Ziyang Zheng", "Siming Dai", "Guoyong Yin", "Shujie Zhao"], "journal": "Frontiers in medicine", "year": 2023, "abstract": "Background: The pathophysiology of bone defects (BDs) is complex, and the treatment for bone defects, in particular massive bone defects, remains a major clinical challenge. Our study was conducted to explore the molecular events related to the progression of bone defects a common clinical condition.\nMethods: First, microarray data of GSE20980 were obtained from the Gene Expression Omnibus (GEO) database, where 33 samples in total were used to analyze the molecular biological processes related to bone defects. Next, the original data were normalized and differentially expressed genes (DEGs) were identified. Additionally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. Finally, a protein-protein interaction (PPI) network was constructed and the trends of the different genes were confirmed.\nResults: Compared with the samples of non-critical size defects (NCSD), the samples of critical size defects (CSD) had 2057, 827, and 1,024 DEGs at 7, 14, and 21 days post injury, respectively. At day 7, the DEGs were significantly enriched in metabolic pathways, at day 14 the DEGs were predominantly enriched in G-protein coupled signaling pathways and the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway, and at day 21 the DEGs were mainly enriched in circadian entrainment and synaptic-related functions. The PPI network showed similar results. Quantitative real-time PCR (qRT-PCR) and western blot (WB) were performed to validate the partial results of sequencing.\nConclusion: This study provides some clues about the molecular mechanism behind bone defects, which should contribute to scientific research and clinical treatment of this condition.", "claims": [{"id": "claim-method", "statement": "The Student’s t-test was used to identify DEGs with an average fold-change of >2.0, and p < 0.05 was considered to indicate a statistically significant difference.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37359021", "locator": "sections[5] \"Identification and analysis of differentially expressed genes\" paragraph 2", "quote": "The Student’s t-test was used to identify DEGs with an average fold-change of >2.0, and p < 0.05 was considered to indicate a statistically significant difference."}], "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 below: https://www.ncbi.nlm.nih.gov/geo/, GSE20980.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37359021", "locator": "sections[18] \"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 below: https://www.ncbi.nlm.nih.gov/geo/, GSE20980."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Compared with NCSD samples, CSD samples had 2,057, 827, and 1,024 differentially expressed genes at 7, 14, and 21 days post injury, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37359021", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Compared with the samples of non-critical size defects (NCSD), the samples of critical size defects (CSD) had 2057, 827, and 1,024 DEGs at 7, 14, and 21 days post injury, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Compared with NCSD samples, CSD samples had 2,057, 827, and 1,024 differentially expressed genes at 7, 14, and 21 days post injury, respectively.", "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:37359021"], "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:GSE20980"], "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:GSE20980"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37359021", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmed.2023.1157099", "sha256": "sha256:58ef4f91a9ec76324fdfa5173904bc2da622bc738dadb5b4b2c52071be9e9830", "bytes": 36355, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmed.2023.1157099", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10286739", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20980", "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=GSE20980", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20980", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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