[Bioinformatics analysis of expression and function of EXD3 gene in gastric cancer].

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30890511", "kind": "science-record", "revision": 4, "content_hash": "sha256:ffc4ffb895f46dbf6d2193b55f2aa3a11c8b436d50baa551075523b8558bc8d7", "created_at": "2026-11-01T17:32:42Z", "updated_at": "2026-11-01T22:00:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "[Bioinformatics analysis of expression and function of EXD3 gene in gastric cancer].", "doi": "10.12122/j.issn.1673-4254.2019.02.14", "pmid": "30890511", "authors": ["Dengzhong Sun", "Mulin Liu", "Fuxin Huang", "Fuxin Huang"], "journal": "Nan fang yi ke da xue xue bao = Journal of Southern Medical University", "year": 2019, "abstract": "OBJECTIVE: To investigate the differentially expressed genes between gastric cancer and normal gastric mucosa by bioinformatics analysis, identify the important gene participating in the occurrence and progression of gastric cancer, and predict the functions of these genes.\nMETHODS: The gene expression microarray data GSE100935 (including 18 gastric cancer samples and normal gastric mucosal tissues) downloaded from the GEO expression profile database were analyzed using Morpheus to obtain the differentially expressed genes in gastric cancer, and a cluster analysis heat map was constructed. The online database UALCAN was used to obtain the expression levels of these differentially expressed genes in gastric cancer and normal gastric mucosa. The prognostic value of the differentially expressed genes in gastric cancer was evaluated with Kaplan-Meier survival analysis. GO functional enrichment analysis was performed using Fun-Rich software, and the STRING database was exploited to establish a PPI network for the differentially expressed genes.\nRESULTS: A total of 45119 differentially expressed genes were identified from GSE100935 microarray data. Analysis with UALCAN showed an obvious high expression of EXD3 gene in gastric cancer, and survival analysis suggested that a high expression level of EXD3 was associated with a poorer prognosis of the patients with gastric cancer. GO functional enrichment analysis found that the differentially expressed genes in gastric cancer were involved mainly in the regulation of nucleotide metabolism and the activity of transcription factors in the cancer cells.\nCONCLUSIONS: EXD3 may be a potential oncogene in gastric cancer possibly in relation to DNA damage repair. The up-regulation of EXD3 plays an important role in the development and prognosis of gastric cancer, and may serve as an important indicator for prognostic evaluation of the patients.", "claims": [{"id": "claim-method", "statement": "利用Morpheus在线软件分析基因芯片GSE100935的数据，获得在胃癌与正常胃粘膜组织中存在差异表达的基因，并构建聚类分析热图", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30890511", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "利用Morpheus在线软件分析基因芯片GSE100935的数据，获得在胃癌与正常胃粘膜组织中存在差异表达的基因，并构建聚类分析热图"}], "state": "complete"}, {"id": "claim-data-access", "statement": "从GEO表达谱数据库中下载表达谱基因芯片数据GSE100935（包括18例胃癌样本及正常胃粘膜组织）", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30890511", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "从GEO表达谱数据库中下载表达谱基因芯片数据GSE100935（包括18例胃癌样本及正常胃粘膜组织）"}], "state": "complete"}, {"id": "claim-target-result", "statement": "EXD3可能是胃癌中潜在的癌基因，可能与DNA损伤修复有关，其表达上调在胃癌的发生发展及预后过程发挥重要作用，并有望成为判断胃癌患者预后的重要的生物学指标。", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:30890511", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "EXD3可能是胃癌中潜在的癌基因，可能与DNA损伤修复有关，其表达上调在胃癌的发生发展及预后过程发挥重要作用，并有望成为判断胃癌患者预后的重要的生物学指标。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "EXD3可能是胃癌中潜在的癌基因，可能与DNA损伤修复有关，其表达上调在胃癌的发生发展及预后过程发挥重要作用，并有望成为判断胃癌患者预后的重要的生物学指标。", "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:30890511"], "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:GSE100935"], "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:GSE100935"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30890511", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12122/j.issn.1673-4254.2019.02.14", "sha256": "sha256:0f93caeb6a9e4312a37d8f888f28e249aab75bb175d6b19edc4f8bc486288c08", "bytes": 544, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12122/j.issn.1673-4254.2019.02.14", "version": null, "note": "Full article fetched from PMC; 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