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Identification of genomic functional hotspots with copy number alteration in liver cancer

Copy number alterations (CNAs) can be observed in most of cancer patients. Several oncogenes and tumor suppressor genes with CNAs have been identified in different kinds of tumor. However, the systematic survey of CNA-affected functions is still lack. By employing systems biology approaches, instead...

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Autores principales: Hsiao, Tzu-Hung, Chen, Hung-I Harry, Roessler, Stephanie, Wang, Xin Wei, Chen, Yidong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833309/
https://www.ncbi.nlm.nih.gov/pubmed/24160471
http://dx.doi.org/10.1186/1687-4153-2013-14
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author Hsiao, Tzu-Hung
Chen, Hung-I Harry
Roessler, Stephanie
Wang, Xin Wei
Chen, Yidong
author_facet Hsiao, Tzu-Hung
Chen, Hung-I Harry
Roessler, Stephanie
Wang, Xin Wei
Chen, Yidong
author_sort Hsiao, Tzu-Hung
collection PubMed
description Copy number alterations (CNAs) can be observed in most of cancer patients. Several oncogenes and tumor suppressor genes with CNAs have been identified in different kinds of tumor. However, the systematic survey of CNA-affected functions is still lack. By employing systems biology approaches, instead of examining individual genes, we directly identified the functional hotspots on human genome. A total of 838 hotspots on human genome with 540 enriched Gene Ontology functions were identified. Seventy-six aCGH array data of hepatocellular carcinoma (HCC) tumors were employed in this study. A total of 150 regions which putatively affected by CNAs and the encoded functions were identified. Our results indicate that two immune related hotspots had copy number alterations in most of patients. In addition, our data implied that these immune-related regions might be involved in HCC oncogenesis. Also, we identified 39 hotspots of which copy number status were associated with patient survival. Our data implied that copy number alterations of the regions may contribute in the dysregulation of the encoded functions. These results further demonstrated that our method enables researchers to survey biological functions of CNAs and to construct regulation hypothesis at pathway and functional levels.
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spelling pubmed-38333092013-11-28 Identification of genomic functional hotspots with copy number alteration in liver cancer Hsiao, Tzu-Hung Chen, Hung-I Harry Roessler, Stephanie Wang, Xin Wei Chen, Yidong EURASIP J Bioinform Syst Biol Research Copy number alterations (CNAs) can be observed in most of cancer patients. Several oncogenes and tumor suppressor genes with CNAs have been identified in different kinds of tumor. However, the systematic survey of CNA-affected functions is still lack. By employing systems biology approaches, instead of examining individual genes, we directly identified the functional hotspots on human genome. A total of 838 hotspots on human genome with 540 enriched Gene Ontology functions were identified. Seventy-six aCGH array data of hepatocellular carcinoma (HCC) tumors were employed in this study. A total of 150 regions which putatively affected by CNAs and the encoded functions were identified. Our results indicate that two immune related hotspots had copy number alterations in most of patients. In addition, our data implied that these immune-related regions might be involved in HCC oncogenesis. Also, we identified 39 hotspots of which copy number status were associated with patient survival. Our data implied that copy number alterations of the regions may contribute in the dysregulation of the encoded functions. These results further demonstrated that our method enables researchers to survey biological functions of CNAs and to construct regulation hypothesis at pathway and functional levels. BioMed Central 2013 2013-10-25 /pmc/articles/PMC3833309/ /pubmed/24160471 http://dx.doi.org/10.1186/1687-4153-2013-14 Text en Copyright © 2013 Hsiao et al.; licensee Springer. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Hsiao, Tzu-Hung
Chen, Hung-I Harry
Roessler, Stephanie
Wang, Xin Wei
Chen, Yidong
Identification of genomic functional hotspots with copy number alteration in liver cancer
title Identification of genomic functional hotspots with copy number alteration in liver cancer
title_full Identification of genomic functional hotspots with copy number alteration in liver cancer
title_fullStr Identification of genomic functional hotspots with copy number alteration in liver cancer
title_full_unstemmed Identification of genomic functional hotspots with copy number alteration in liver cancer
title_short Identification of genomic functional hotspots with copy number alteration in liver cancer
title_sort identification of genomic functional hotspots with copy number alteration in liver cancer
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3833309/
https://www.ncbi.nlm.nih.gov/pubmed/24160471
http://dx.doi.org/10.1186/1687-4153-2013-14
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