OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions.
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions.
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OpenAnnotate：用于注释基因组区域染色质可及性的网络服务器
DOI：
10.1093/nar/gkab337
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发表时间：
2021-07-02
影响因子：
14.9
通讯作者：
Jiang R
中科院分区：
文献类型：
--
作者：
Chen S;Liu Q;Cui X;Feng Z;Li C;Wang X;Zhang X;Wang Y;Jiang R
摘要染色质可及性作为活性DNA调控元件的有力标志，为理解调控机制提供了有价值的信息。高通量方法的革命在公共存储库中积累了大量的染色质可访问性配置文件。然而，这些数据的利用受到繁琐的收集、耗时的处理和基因组区域的人工染色质可访问性(开放性)注释的阻碍。为了填补这一空白，我们开发了OpenAnnotate(http://health.tsinghua.edu.cn/openannotate/))作为第一个网络服务器，用于有效地注释各种生物样本类型、组织和生物系统中大量基因组区域的开放性。除了来自614种生物样本类型的2729个全面概况的注释资源外，OpenAnnotate还提供用户友好的功能、超高效的计算、实时浏览、直观的可视化和精心设计的应用笔记本。与现有的数据库和工具箱相比，我们通过有效地揭示细胞类型特异性、识别调控元件和3D染色质接触、破译基因功能关系、推断转录因子的功能以及前所未有地促进单细胞数据分析，展示了其独特的优势。我们预计OpenAnnotate将为研究人员构建更全面的视角来理解调控机制提供一条有希望的途径。
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.
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影响因子：
14.9
作者：
Howe KL;Achuthan P;Allen J;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Azov AG;Bennett R;Bhai J;Billis K;Boddu S;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;El Houdaigui B;Fatima R;Gall A;Garcia Giron C;Grego T;Guijarro-Clarke C;Haggerty L;Hemrom A;Hourlier T;Izuogu OG;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Gonzalez Martinez J;Marugán JC;Maurel T;McMahon AC;Mohanan S;Moore B;Muffato M;Oheh DN;Paraschas D;Parker A;Parton A;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Steed E;Szpak M;Szuba M;Taylor K;Thormann A;Threadgold G;Walts B;Winterbottom A;Chakiachvili M;Chaubal A;De Silva N;Flint B;Frankish A;Hunt SE;IIsley GR;Langridge N;Loveland JE;Martin FJ;Mudge JM;Morales J;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Cunningham F;Yates AD;Zerbino DR;Flicek P
通讯作者：
Flicek P
RA3 是一种用于单细胞表观遗传表征的参考指导方法
影响因子：
16.6
作者：
Chen S;Yan G;Zhang W;Li J;Jiang R;Lin Z
通讯作者：
Lin Z
影响因子：
64.8
作者：
Gaspar-Maia A;Alajem A;Polesso F;Sridharan R;Mason MJ;Heidersbach A;Ramalho-Santos J;McManus MT;Plath K;Meshorer E;Ramalho-Santos M
通讯作者：
Ramalho-Santos M
影响因子：
30.8
作者：
John S;Sabo PJ;Thurman RE;Sung MH;Biddie SC;Johnson TA;Hager GL;Stamatoyannopoulos JA
通讯作者：
Stamatoyannopoulos JA
影响因子：
30.8
作者：
Kircher, Martin;Witten, Daniela M.;Jain, Preti;O'Roak, Brian J.;Cooper, Gregory M.;Shendure, Jay
通讯作者：
Shendure, Jay