KMS Of Academy of mathematics and systems sciences, CAS
| OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions | |
Chen, Shengquan1; Liu, Qiao1; Cui, Xuejian1; Feng, Zhanying2,3; Li, Chunquan4; Wang, Xiaowo1; Zhang, Xuegong1; Wang, Yong2,3 ; Jiang, Rui1
| |
| 2021-07-02 | |
| Source Publication | NUCLEIC ACIDS RESEARCH
 |
| ISSN | 0305-1048 |
| Volume | 49Issue:W1Pages:W483-W490 |
| Abstract | 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. |
| DOI | 10.1093/nar/gkab337 |
| Indexed By | SCI |
| Language | 英语 |
| Funding Project | 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 Research Area | Biochemistry & Molecular Biology |
| WOS Subject | Biochemistry & Molecular Biology |
| WOS ID | WOS:000672775800062 |
| Publisher | OXFORD UNIV PRESS |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/58963 |
| Collection | 应用数学研究所 |
| Corresponding Author | Jiang, Rui |
| Affiliation | 1.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 2.Chinese Acad Sci, Acad Math & Syst Sci, CEMS, NCMIS,MDIS, Beijing 100190, Peoples R China 3.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China 4.Harbin Med Univ, Sch Med Informat, Daqing Campus, Daqing 163319, Peoples R China |
| Recommended Citation 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. |
| Files in This Item: | There are no files associated with this item. | |||||
Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.
Edit Comment