Comprehensive and computational analysis of genes in human umbilical vein endothelial cells responsive to X-irradiation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27275413", "kind": "science-record", "revision": 6, "content_hash": "sha256:686b42b30e9edef5eaf5380f120676aff53d536a295a64f9979d47ab6bfd5854", "created_at": "2026-11-01T15:40:18Z", "updated_at": "2026-11-01T21:20:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive and computational analysis of genes in human umbilical vein endothelial cells responsive to X-irradiation.", "doi": "10.1016/j.gdata.2016.05.007", "pmid": "27275413", "authors": ["Yukihiro Furusawa", "Qing-Li Zhao", "Yuichi Hattori", "Yoshiaki Tabuchi", "Toshiyasu Iwasaki", "Takaharu Nomura", "Takashi Kondo"], "journal": "Genomics data", "year": 2016, "abstract": "Radiation exposure such as A-bomb or radiation therapy is considered a major health-risk factor for cardiovascular disease. In order to understand the molecular mechanisms underlying the inflammatory reaction frequently encountered in the vascular system after exposure to ionizing radiation, we carried out a global scale microarray and computational gene expression analyses on human umbilical endothelial cells (HUVECs) exposed to X-ray (2.5 Gy). The gene ontology analysis revealed that the down-regulated genes were associated with cell cycle regulation, whereas the up-regulated genes were associated with inflammatory responses, in particular, the type 1 interferon response. The computational analysis using ingenuity pathway analysis also identified a gene network containing the interferon response factor 7 (IRF7) and its transcriptional targets such as interferon-induced transcripts (IFITs) and Mx1, which have been known to be associated with inflammation in endothelial cells. The up-regulated genes and the gene network identified here may explain the inflammatory response induced by X-irradiation. These findings uncover part of the molecular basis of the mechanism(s) of the inflammatory disorder in response to X-irradiation in HUVECs. The dataset is publicly available at the Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE76484.", "claims": [{"id": "claim-method", "statement": "Principal component analysis (PCA), gene ontology (GO) analysis, and hierarchical clustering from the obtained normalized intensity data were performed using GeneSpring® software (Agilent).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27275413", "locator": "sections[8] \"Gene expression analysis\" paragraph 3", "quote": "Principal component analysis (PCA), gene ontology (GO) analysis, and hierarchical clustering from the obtained normalized intensity data were performed using GeneSpring® software (Agilent)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset is publicly available at the Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE76484.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27275413", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The dataset is publicly available at the Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE76484."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Global-scale microarray and computational gene-expression analysis showed that 2.5 Gy X-irradiation induced a type-1-interferon-associated inflammatory response in HUVECs involving IRF7 and its transcriptional targets, with the source data deposited in GEO under accession GSE76484.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27275413", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The gene ontology analysis revealed that the down-regulated genes were associated with cell cycle regulation, whereas the up-regulated genes were associated with inflammatory responses, in particular, the type 1 interferon response."}, {"asset": "source:pmid:27275413", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The computational analysis using ingenuity pathway analysis also identified a gene network containing the interferon response factor 7 (IRF7) and its transcriptional targets such as interferon-induced transcripts (IFITs) and Mx1, which have been known to be associated with inflammation in endothelial cells."}, {"asset": "source:pmid:27275413", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The dataset is publicly available at the Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE76484."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Global-scale microarray and computational gene-expression analysis showed that 2.5 Gy X-irradiation induced a type-1-interferon-associated inflammatory response in HUVECs involving IRF7 and its transcriptional targets, with the source data deposited in GEO under accession GSE76484.", "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:27275413"], "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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