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

doi:10.1093/nar/gkab337

	OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions
	Chen, Shengquan 4; Liu, Qiao 4; Cui, Xuejian 4; Feng, Zhanying 2,3; Li, Chunquan 1; Wang, Xiaowo 4; Zhang, Xuegong 4; Wang, Yong 2,3; Jiang, Rui 4
刊名	NUCLEIC ACIDS RESEARCH
	2021-07-02
卷号	49 期号:W1 页码:W483-W490
ISSN号	0305-1048
DOI	10.1093/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
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000672775800062
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/58962]
专题	中国科学院数学与系统科学研究院
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.