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CircleBase: an integrated resource and analysis platform for human eccDNAs
Rapid advances in high-throughput sequencing technologies have led to the discovery of thousands of extrachromosomal circular DNAs (eccDNAs) in the human genome. Loss-of-function experiments are difficult to conduct on circular and linear chromosomes, as they usually overlap. Hence, it is challengin...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728191/ https://www.ncbi.nlm.nih.gov/pubmed/34792166 http://dx.doi.org/10.1093/nar/gkab1104 |
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author | Zhao, Xiaolu Shi, Leisheng Ruan, Shasha Bi, Wenjian Chen, Yifan Chen, Lin Liu, Yifan Li, Mingkun Qiao, Jie Mao, Fengbiao |
author_facet | Zhao, Xiaolu Shi, Leisheng Ruan, Shasha Bi, Wenjian Chen, Yifan Chen, Lin Liu, Yifan Li, Mingkun Qiao, Jie Mao, Fengbiao |
author_sort | Zhao, Xiaolu |
collection | PubMed |
description | Rapid advances in high-throughput sequencing technologies have led to the discovery of thousands of extrachromosomal circular DNAs (eccDNAs) in the human genome. Loss-of-function experiments are difficult to conduct on circular and linear chromosomes, as they usually overlap. Hence, it is challenging to interpret the molecular functions of eccDNAs. Here, we present CircleBase (http://circlebase.maolab.org), an integrated resource and analysis platform used to curate and interpret eccDNAs in multiple cell types. CircleBase identifies putative functional eccDNAs by incorporating sequencing datasets, computational predictions, and manual annotations. It classifies them into six sections including targeting genes, epigenetic regulations, regulatory elements, chromatin accessibility, chromatin interactions, and genetic variants. The eccDNA targeting and regulatory networks are displayed by informative visualization tools and then prioritized. Functional enrichment analyses revealed that the top-ranked cancer cell eccDNAs were enriched in oncogenic pathways such as the Ras and PI3K-Akt signaling pathways. In contrast, eccDNAs from healthy individuals were not significantly enriched. CircleBase provides a user-friendly interface for searching, browsing, and analyzing eccDNAs in various cell/tissue types. Thus, it is useful to screen for potential functional eccDNAs and interpret their molecular mechanisms in human cancers and other diseases. |
format | Online Article Text |
id | pubmed-8728191 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87281912022-01-05 CircleBase: an integrated resource and analysis platform for human eccDNAs Zhao, Xiaolu Shi, Leisheng Ruan, Shasha Bi, Wenjian Chen, Yifan Chen, Lin Liu, Yifan Li, Mingkun Qiao, Jie Mao, Fengbiao Nucleic Acids Res Database Issue Rapid advances in high-throughput sequencing technologies have led to the discovery of thousands of extrachromosomal circular DNAs (eccDNAs) in the human genome. Loss-of-function experiments are difficult to conduct on circular and linear chromosomes, as they usually overlap. Hence, it is challenging to interpret the molecular functions of eccDNAs. Here, we present CircleBase (http://circlebase.maolab.org), an integrated resource and analysis platform used to curate and interpret eccDNAs in multiple cell types. CircleBase identifies putative functional eccDNAs by incorporating sequencing datasets, computational predictions, and manual annotations. It classifies them into six sections including targeting genes, epigenetic regulations, regulatory elements, chromatin accessibility, chromatin interactions, and genetic variants. The eccDNA targeting and regulatory networks are displayed by informative visualization tools and then prioritized. Functional enrichment analyses revealed that the top-ranked cancer cell eccDNAs were enriched in oncogenic pathways such as the Ras and PI3K-Akt signaling pathways. In contrast, eccDNAs from healthy individuals were not significantly enriched. CircleBase provides a user-friendly interface for searching, browsing, and analyzing eccDNAs in various cell/tissue types. Thus, it is useful to screen for potential functional eccDNAs and interpret their molecular mechanisms in human cancers and other diseases. Oxford University Press 2021-11-18 /pmc/articles/PMC8728191/ /pubmed/34792166 http://dx.doi.org/10.1093/nar/gkab1104 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Zhao, Xiaolu Shi, Leisheng Ruan, Shasha Bi, Wenjian Chen, Yifan Chen, Lin Liu, Yifan Li, Mingkun Qiao, Jie Mao, Fengbiao CircleBase: an integrated resource and analysis platform for human eccDNAs |
title | CircleBase: an integrated resource and analysis platform for human eccDNAs |
title_full | CircleBase: an integrated resource and analysis platform for human eccDNAs |
title_fullStr | CircleBase: an integrated resource and analysis platform for human eccDNAs |
title_full_unstemmed | CircleBase: an integrated resource and analysis platform for human eccDNAs |
title_short | CircleBase: an integrated resource and analysis platform for human eccDNAs |
title_sort | circlebase: an integrated resource and analysis platform for human eccdnas |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728191/ https://www.ncbi.nlm.nih.gov/pubmed/34792166 http://dx.doi.org/10.1093/nar/gkab1104 |
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