题名 | MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification |
作者 | |
通讯作者 | Tian, Simon Zhongyuan; Chen, Wei; Zheng, Meizhen |
发表日期 | 2022-11-19
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DOI | |
发表期刊 | |
ISSN | 1467-5463
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EISSN | 1477-4054
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摘要 | The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies not only offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for multi-way chromatin interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell-cycle-associated genes. Taken together, MCIBox represents an invaluable tool for the study of multiple chromatin interactions and inaugurates a previously unappreciated view of 3D genome structure. |
关键词 | |
相关链接 | [来源记录] |
收录类别 | |
语种 | 英语
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学校署名 | 第一
; 通讯
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资助项目 | National Natural Science Foundation of China[32170644]
; Shenzhen Innovation Committee of Science and Technology[ZDSYS20200811144002008]
; Ministry of Education Tier II grant[T2EP30120-0020]
; Polish National Science Centre[
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WOS研究方向 | Biochemistry & Molecular Biology
; Mathematical & Computational Biology
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WOS类目 | Biochemical Research Methods
; Mathematical & Computational Biology
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WOS记录号 | WOS:000852754600001
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出版者 | |
ESI学科分类 | COMPUTER SCIENCE
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来源库 | Web of Science
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出版状态 | 正式出版
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引用统计 |
被引频次[WOS]:2
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成果类型 | 期刊论文 |
条目标识符 | http://sustech.caswiz.com/handle/2SGJ60CL/401507 |
专题 | 生命科学学院 生命科学学院_生物系 |
作者单位 | 1.Southern Univ Sci & Technol, Sch Life Sci, Shenzhen, Peoples R China 2.Huazhong Agr Univ, Coll Informat, Wuhan, Peoples R China 3.Natl Univ Singapore, Canc Sci Inst Singapore, Singapore, Singapore 4.Nanyang Technol Univ, Sch Biol Sci, Singapore, Singapore 5.ASTAR, Inst Mol & Cell Biol, Singapore, Singapore 6.Univ Warsaw Technol, Lab Funt & Struct & Coputat Genom, Fac Math & Infomat Sci, Warsaw, Poland 7.Univ Warsaw, Lab Funt & Struct & Coputat Genom, Ctr New Technol, Warsaw, Poland 8.Southern Univ Sci Technol, Sch Life Sci, Chair Dept Biol, Syst Biol, Shenzhen, Peoples R China |
第一作者单位 | 生命科学学院 |
通讯作者单位 | 生命科学学院; 生物系 |
第一作者的第一单位 | 生命科学学院 |
推荐引用方式 GB/T 7714 |
Tian, Simon Zhongyuan,Li, Guoliang,Ning, Duo,et al. MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification[J]. BRIEFINGS IN BIOINFORMATICS,2022.
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APA |
Tian, Simon Zhongyuan.,Li, Guoliang.,Ning, Duo.,Jing, Kai.,Xu, Yewen.,...&Zheng, Meizhen.(2022).MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification.BRIEFINGS IN BIOINFORMATICS.
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MLA |
Tian, Simon Zhongyuan,et al."MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification".BRIEFINGS IN BIOINFORMATICS (2022).
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条目包含的文件 | ||||||
文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | 操作 | |
MCIBOX_bbac380.pdf(2476KB) | -- | -- | 限制开放 | -- |
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