DNA Microarray Analysis in Screening Features of Genes Involved in Spinal Cord Injury.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27160807", "kind": "science-record", "revision": 9, "content_hash": "sha256:2289524cd03649ef769b20055805e045542d16781d26dc9efbb03930ffd386aa", "created_at": "2026-11-01T15:40:18Z", "updated_at": "2026-11-01T22:42:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "DNA Microarray Analysis in Screening Features of Genes Involved in Spinal Cord Injury.", "doi": "10.12659/msm.895889", "pmid": "27160807", "authors": ["Yugang Liu", "Ying Wang", "Zhaowei Teng", "Xiufeng Zhang", "Min Ding", "Zhaojun Zhang", "Junli Chen", "Yanli Xu"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2016, "abstract": "BACKGROUND Spinal cord injury (SCI) is the most critical complication of spinal injury. We aimed to identify differentially expressed genes (DEGs) and to find associated pathways that may function as targets for SCI prognosis and therapy. MATERIAL AND METHODS Seven gene microarray expression profiles, downloaded from the GEO database (ID: GSE33886), were used to screen the DEGs of leg tissue and to compare these between SCI patients and corresponding normal specimens. Then, GO enrichment analysis was performed on these selected DEGs. Afterwards, interactions among these DEGs were analyzed by String database and then a PPI network was constructed to obtain topology character and modules in the PPI network. Finally, roles of the critical proteins in the pathway were explained by comparing the enrichment results of the genes in sub-modules and all the DEGs. RESULTS A total of 113 DEGs were determined. We found that 21 up-regulated genes were enriched in 7 biological processes, while 9 down-regulated genes were significantly enriched in 4 KEGG pathways. The PPI network was constructed, including 40 interacting genes and 73 interactions. Three obvious function modules were identified by exploring the PPI network, and ACTC1 was identified as the critical protein in the 3 enriched signal pathways. However, no obvious difference was found in the signal pathway in which both the 11 genes in module 1 and all 113 DEGs participated. CONCLUSIONS Core proteins in the signal pathway associated with spinal cord injury may serve as potential prognostic and predictive markers for the diagnosis and treatment of spinal cord injury in clinical applications.", "claims": [{"id": "claim-method", "statement": "DEGs that were significantly differentially expressed among the mesenchymal stem cell samples from SCI patients and the matched normal tissues were screened out by use of the LIMMA package [14] in R language.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27160807", "locator": "sections[5] \"Screening of differentially expressed genes\" paragraph 2", "quote": "DEGs that were significantly differentially expressed among the mesenchymal stem cell samples from SCI patients and the matched normal tissues were screened out by use of the LIMMA package [14] in R language."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray expression profiles of spinal cord injury were extracted from the GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database under the accession number of GSE33886 [11,12]. A total of 7 specimens divided into 2 groups were available for the analysis, including 4 samples from normal vastus lateralis leg tissues and 3 specimens from leg tissues of patients with spinal cord injury. The data platform used was Affymetrix Human Gene 1.0 ST Array.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27160807", "locator": "sections[3] \"Data source\" paragraph 2", "quote": "The microarray expression profiles of spinal cord injury were extracted from the GEO (Gene Expression Omnibus, http://www.ncbi.nlm.nih.gov/geo/) database under the accession number of GSE33886 [11,12]. A total of 7 specimens divided into 2 groups were available for the analysis, including 4 samples from normal vastus lateralis leg tissues and 3 specimens from leg tissues of patients with spinal cord injury. The data platform used was Affymetrix Human Gene 1.0 ST Array."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 113 differentially expressed genes by screening seven GEO GSE33886 microarray expression profiles with LIMMA.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27160807", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Seven gene microarray expression profiles, downloaded from the GEO database (ID: GSE33886), were used to screen the DEGs of leg tissue and to compare these between SCI patients and corresponding normal specimens."}, {"asset": "source:pmid:27160807", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 113 DEGs were determined."}, {"asset": "source:pmid:27160807", "locator": "sections[5] \"Screening of differentially expressed genes\" paragraph 2", "quote": "DEGs that were significantly differentially expressed among the mesenchymal stem cell samples from SCI patients and the matched normal tissues were screened out by use of the LIMMA package [14] in R language."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 113 differentially expressed genes by screening seven GEO GSE33886 microarray expression profiles with LIMMA.", "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:27160807"], "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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MATERIAL AND METHODS Seven gene microarray expression profiles, downloaded from the GEO"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["DEGs that were significantly differentially expressed among the mesenchymal stem cell samples from SCI patients and the matched normal tissues were screened out by use of the LIMMA package [14] in R language."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}