Identification of Differentially Expressed Gene after Femoral Fracture via Microarray Profiling.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25110652", "kind": "science-record", "revision": 8, "content_hash": "sha256:bad43f42503a9478dc82603a99007540d23c92dc27c69295229e87015d30c3cd", "created_at": "2026-11-01T15:40:05Z", "updated_at": "2026-11-01T21:58:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Differentially Expressed Gene after Femoral Fracture via Microarray Profiling.", "doi": "10.1155/2014/208751", "pmid": "25110652", "authors": ["Donggen Zhong"], "journal": "International journal of genomics", "year": 2014, "abstract": "We aimed to investigate differentially expressed genes (DEGs) in different stages after femoral fracture based on rat models, providing the basis for the treatment of sport-related fractures. Gene expression data GSE3298 was downloaded from Gene Expression Omnibus (GEO), including 16 chips. All femoral fracture samples were classified into earlier fracture stage and later fracture stage. Total 87 DEGs simultaneously occurred in two stages, of which 4 genes showed opposite expression tendency. Out of the 4 genes, Rest and Cst8 were hub nodes in protein-protein interaction (PPI) network. The GO (Gene Ontology) function enrichment analysis verified that nutrition supply related genes were enriched in the earlier stage and neuron growth related genes were enriched in the later stage. Calcium signaling pathway was the most significant pathway in earlier stage; in later stage, DEGs were enriched into 2 neurodevelopment-related pathways. Analysis of Pearson's correlation coefficient showed that a total of 3,300 genes were significantly associated with fracture time, none of which was overlapped with identified DEGs. This study suggested that Rest and Cst8 might act as potential indicators for fracture healing. Calcium signaling pathway and neurodevelopment-related pathways might be deeply involved in bone healing after femoral fracture.", "claims": [{"id": "claim-method", "statement": "A Pearson correlation coefficient was calculated between expression level of every expressed gene after fracture and fracture time via cor.test in R language [22]. The P < 0.05 was chosen as cut-off criterion.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25110652", "locator": "sections[8] \"2.6. Correlation Analysis\" paragraph 2", "quote": "A Pearson correlation coefficient was calculated between expression level of every expressed gene after fracture and fracture time via cor.test in R language [22]. The P < 0.05 was chosen as cut-off criterion."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA expression profiling data was obtained from the research of Meyer et al., which were displayed in GEO (http://www.ncbi.nlm.nih.gov/geo/) database (ID: GSE3298) [12]. The microarray data in CEL files were downloaded from GEO database, including 16 chips, converted into fluorescence intensity values and standardized via the robust multiarray average (RMA) method [14].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25110652", "locator": "sections[3] \"2.1. Microarray Data\" paragraph 2", "quote": "The mRNA expression profiling data was obtained from the research of Meyer et al., which were displayed in GEO (http://www.ncbi.nlm.nih.gov/geo/) database (ID: GSE3298) [12]."}, {"asset": "source:pmid:25110652", "locator": "sections[4] \"2.2. Data Preprocess\" paragraph 2", "quote": "The microarray data in CEL files were downloaded from GEO database, including 16 chips, converted into fluorescence intensity values and standardized via the robust multiarray average (RMA) method [14]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GSE3298 downloaded from GEO and Pearson's correlation analysis, the study identified 3,300 genes significantly associated with fracture time, none of which overlapped with the identified DEGs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25110652", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Gene expression data GSE3298 was downloaded from Gene Expression Omnibus (GEO), including 16 chips."}, {"asset": "source:pmid:25110652", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Analysis of Pearson's correlation coefficient showed that a total of 3,300 genes were significantly associated with fracture time, none of which was overlapped with identified DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GSE3298 downloaded from GEO and Pearson's correlation analysis, the study identified 3,300 genes significantly associated with fracture time, none of which overlapped with the identified DEGs.", "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:25110652"], "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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