MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing.
MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing.
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MethSMRT：单分子实时测序生成的 DNA N6-甲基腺嘌呤和 N4-甲基胞嘧啶的综合数据库
DOI：
10.1093/nar/gkw950
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发表时间：
2017-01-04
影响因子：
14.9
通讯作者：
Xie Z
中科院分区：
文献类型：
--
作者：
Ye P;Luan Y;Chen K;Liu Y;Xiao C;Xie Z
DNA甲基化是表观遗传修饰的重要类型，其中5-甲基胞嘧啶(5mC)、6-亚甲基腺嘌呤(6mA)和4-甲基胞嘧啶(4mC)是最常见的类型。之前的工作主要集中在 5mC 上，为通过 DNA 甲基化进行表观遗传调控提供了宝贵的见解。最近开发的单分子实时 (SMRT) 测序技术提供了独特的机会，以单核苷酸分辨率检测研究较少的 DNA 6mA 和 4mC 修饰。随着生成的 SMRT 测序数据量迅速增加，越来越需要从这些数据集中系统地探索 DNA 6mA 和 4mC 修饰。 MethSMRT 是第一个托管 DNA 6mA 和 4mC 甲基化组的资源。所有数据集均使用相同的分析流程和相同的质量控制进行处理。当前版本的数据库提供了一个存储、浏览、搜索和下载156个物种的全表观基因组甲基化图谱的平台，包括拟南芥、线虫、果蝇、小鼠和酵母等7种真核生物以及149种原核生物。它还提供基因组浏览器来可视化甲基化位点和相关信息，例如单核苷酸多态性 (SNP) 和基因组注释。此外，该数据库还提供了 6mA 和 4mC 甲基化组统计数据的快速汇总以及每个物种的预测甲基化基序。 MethSMRT可在http://sysbio.sysu.edu.cn/methsmrt/公开获取，无使用限制。
DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets. MethSMRT is the first resource hosting DNA 6mA and 4mC methylomes. All the data sets were processed using the same analysis pipeline with the same quality control. The current version of the database provides a platform to store, browse, search and download epigenome-wide methylation profiles of 156 species, including seven eukaryotes such as Arabidopsis, C. elegans, Drosophila, mouse and yeast, as well as 149 prokaryotes. It also offers a genome browser to visualize the methylation sites and related information such as single nucleotide polymorphisms (SNP) and genomic annotation. Furthermore, the database provides a quick summary of statistics of methylome of 6mA and 4mC and predicted methylation motifs for each species. MethSMRT is publicly available at http://sysbio.sysu.edu.cn/methsmrt/ without use restriction.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
N6-甲基脱氧腺苷标记了衣原体中的主动转录起始位点。
影响因子：
64.5
作者：
Fu Y;Luo GZ;Chen K;Deng X;Yu M;Han D;Hao Z;Liu J;Lu X;Dore LC;Weng X;Ji Q;Mets L;He C
通讯作者：
He C
影响因子：
48
作者：
Flusberg, Benjamin A.;Webster, Dale R.;Lee, Jessica H.;Travers, Kevin J.;Olivares, Eric C.;Clark, Tyson A.;Korlach, Jonas;Turner, Stephen W.
通讯作者：
Turner, Stephen W.
影响因子：
14.9
作者：
Ongenaert M;Van Neste L;De Meyer T;Menschaert G;Bekaert S;Van Criekinge W
通讯作者：
Van Criekinge W