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Identification and characteristic analysis of enhancers across 13 major cancer types

Enhancers are often mutated and dysregulated in various diseases such as cancer. By integrating the function annotation of the mammalian genome (FANTOM) enhancers expression profiles and RNA-seq data from The Cancer Genome Atlas (TCGA) of 13 cancers and their corresponding para-cancerous tissues, we...

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Autores principales: Qian, Mingming, Wang, Wenzhu, Zhang, Yana, Zhao, Yi, Quan, Huige, Chen, Yuting, Dai, Xinyue, Guo, Zhiyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982554/
https://www.ncbi.nlm.nih.gov/pubmed/35693214
http://dx.doi.org/10.1093/pcmedi/pbab019
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author Qian, Mingming
Wang, Wenzhu
Zhang, Yana
Zhao, Yi
Quan, Huige
Chen, Yuting
Dai, Xinyue
Guo, Zhiyun
author_facet Qian, Mingming
Wang, Wenzhu
Zhang, Yana
Zhao, Yi
Quan, Huige
Chen, Yuting
Dai, Xinyue
Guo, Zhiyun
author_sort Qian, Mingming
collection PubMed
description Enhancers are often mutated and dysregulated in various diseases such as cancer. By integrating the function annotation of the mammalian genome (FANTOM) enhancers expression profiles and RNA-seq data from The Cancer Genome Atlas (TCGA) of 13 cancers and their corresponding para-cancerous tissues, we systematically identified a total of 4702 significantly differentially expressed (DE) enhancers. Furthermore, a total of 1036 DE genes regulated by DE enhancers were identified. It was found that in these 13 cancers, most (61.13%) enhancers were ubiquitously expressed, whereas DE enhancers were more likely to be tissue-specific expressed, and the DE genes regulated by DE enhancers were significantly enriched in cancer-related pathways. Finally, it was manifested that 74 single nucleotide polymorphisms (SNPs) were located in 37 DE enhancers, and these SNPs affected the gain and loss of functional transcription factor binding sites of 758 transcription factors, which were shown to be highly correlated with tumorigenesis and development.
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spelling pubmed-89825542022-06-10 Identification and characteristic analysis of enhancers across 13 major cancer types Qian, Mingming Wang, Wenzhu Zhang, Yana Zhao, Yi Quan, Huige Chen, Yuting Dai, Xinyue Guo, Zhiyun Precis Clin Med Methodology Enhancers are often mutated and dysregulated in various diseases such as cancer. By integrating the function annotation of the mammalian genome (FANTOM) enhancers expression profiles and RNA-seq data from The Cancer Genome Atlas (TCGA) of 13 cancers and their corresponding para-cancerous tissues, we systematically identified a total of 4702 significantly differentially expressed (DE) enhancers. Furthermore, a total of 1036 DE genes regulated by DE enhancers were identified. It was found that in these 13 cancers, most (61.13%) enhancers were ubiquitously expressed, whereas DE enhancers were more likely to be tissue-specific expressed, and the DE genes regulated by DE enhancers were significantly enriched in cancer-related pathways. Finally, it was manifested that 74 single nucleotide polymorphisms (SNPs) were located in 37 DE enhancers, and these SNPs affected the gain and loss of functional transcription factor binding sites of 758 transcription factors, which were shown to be highly correlated with tumorigenesis and development. Oxford University Press 2021-08-02 /pmc/articles/PMC8982554/ /pubmed/35693214 http://dx.doi.org/10.1093/pcmedi/pbab019 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of the West China School of Medicine & West China Hospital of Sichuan University. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology
Qian, Mingming
Wang, Wenzhu
Zhang, Yana
Zhao, Yi
Quan, Huige
Chen, Yuting
Dai, Xinyue
Guo, Zhiyun
Identification and characteristic analysis of enhancers across 13 major cancer types
title Identification and characteristic analysis of enhancers across 13 major cancer types
title_full Identification and characteristic analysis of enhancers across 13 major cancer types
title_fullStr Identification and characteristic analysis of enhancers across 13 major cancer types
title_full_unstemmed Identification and characteristic analysis of enhancers across 13 major cancer types
title_short Identification and characteristic analysis of enhancers across 13 major cancer types
title_sort identification and characteristic analysis of enhancers across 13 major cancer types
topic Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982554/
https://www.ncbi.nlm.nih.gov/pubmed/35693214
http://dx.doi.org/10.1093/pcmedi/pbab019
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