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OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions

文献类型：期刊论文

作者Chen, Shengquan4; Liu, Qiao4; Cui, Xuejian4; Feng, Zhanying2,3; Li, Chunquan1; Wang, Xiaowo4; Zhang, Xuegong4; Wang, Yong2,3; Jiang, Rui4
刊名NUCLEIC ACIDS RESEARCH
出版日期2021-07-02
卷号49期号:W1页码:W483-W490
ISSN号0305-1048
DOI10.1093/nar/gkab337
英文摘要Chromatin accessibility, as a powerful marker of active DNA regulatory elements, provides valuable information for understanding regulatory mechanisms. The revolution in high-throughput methods has accumulated massive chromatin accessibility profiles in public repositories. Nevertheless, utilization of these data is hampered by cumbersome collection, time-consuming processing, and manual chromatin accessibility (openness) annotation of genomic regions. To fill this gap, we developed OpenAnnotate(http://health.tsinghua.edu.cn/ openannotate/) as the first web server for efficiently annotating openness of massive genomic regions across various biosample types, tissues, and biological systems. In addition to the annotation resource from 2729 comprehensive profiles of 614 biosample types of human and mouse, OpenAnnotate provides user-friendly functionalities, ultra-efficient calculation, real-time browsing, intuitive visualization, and elaborate application notebooks. We show its unique advantages compared to existing databases and toolkits by effectively revealing cell type-specificity, identifying regulatory elements and 3D chromatin contacts, deciphering gene functional relationships, inferring functions of transcription factors, and unprecedentedly promoting single-cell data analyses. We anticipate OpenAnnotate will provide a promising avenue for researchers to construct a more holistic perspective to understand regulatory mechanisms.
资助项目National Key Research and Development Program of China[2018YFC0910404] ; National Natural Science Foundation of China[61873141] ; National Natural Science Foundation of China[61721003] ; National Natural Science Foundation of China[61573207] ; National Natural Science Foundation of China[62003178] ; National Natural Science Foundation of China[12025107] ; National Natural Science Foundation of China[11871463]
WOS研究方向Biochemistry & Molecular Biology
语种英语
WOS记录号WOS:000672775800062
出版者OXFORD UNIV PRESS
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/58962]  
专题应用数学研究所
通讯作者Jiang, Rui
作者单位1.Harbin Med Univ, Sch Med Informat, Daqing Campus, Daqing 163319, Peoples R China
2.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
3.Chinese Acad Sci, Acad Math & Syst Sci, CEMS, NCMIS,MDIS, Beijing 100190, Peoples R China
4.Tsinghua Univ, Beijing Natl Res Ctr Informat Sci & Technol, Bioinformat Div,Key Lab Bioinformat, Ctr Synthet & Syst Biol,Dept Automat,Minist Educ, Beijing 100084, Peoples R China
推荐引用方式
GB/T 7714		 Chen, Shengquan,Liu, Qiao,Cui, Xuejian,et al. OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions[J]. NUCLEIC ACIDS RESEARCH,2021,49(W1):W483-W490.
APA Chen, Shengquan.,Liu, Qiao.,Cui, Xuejian.,Feng, Zhanying.,Li, Chunquan.,...&Jiang, Rui.(2021).OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions.NUCLEIC ACIDS RESEARCH,49(W1),W483-W490.
MLA Chen, Shengquan,et al."OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions".NUCLEIC ACIDS RESEARCH 49.W1(2021):W483-W490.

入库方式： OAI收割

来源：数学与系统科学研究院

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