ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments
ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments
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DOI：
10.1093/nar/gkz945
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
Ballester, Benoit
中科院分区：
文献类型：
--
作者：
Cheneby, Jeanne;Menetrier, Zacharie;Ballester, Benoit
ReMap（http：remap.univ-amu.fr）旨在提供高质量调控区的最大目录，这些调控区是从人类和拟南芥（Arabidopsis thaliana）的DNA结合实验中对数百种转录因子和调控因子进行大规模整合分析而获得的。在2020年的ReMap更新中，我们收集、分析并保留了2764个新的人类ChIP-seq和208个来自公共来源的ChIP-exo数据集。更新后的人类图谱共有5798个数据集，涵盖了总共1135个转录调节因子（TR），目录中有1.65亿个（M）峰。这个ReMap更新带有两个独特的拟南芥调控目录。首先，作为整合509个ChIP-seq和DAP-seq数据集的结果，跨越2.6M峰的372个拟南芥TR的目录。第二，来自286个ChIP-seq数据集整合的450万个峰中的33个组蛋白修饰和变体的目录。所有目录都可以通过Ensembl和UCSC基因组浏览器的跟踪中心获得。此外，此更新还附带了一个新的Web框架，提供了一个交互式用户界面，包括改进的搜索功能。最后，通过使用RESTful API以及用于TRs绑定富集分析工具的新R Shiny接口，可以完全编程访问底层数据。
ReMap (http://remap.univ-amu.fr) aims to provide the largest catalogs of high-quality regulatory regions resulting from a large-scale integrative analysis of hundreds of transcription factors and regulators from DNA-binding experiments in Human and Arabidopsis ( Arabidopsis thaliana). In this 2020 update of ReMap we have collected, analyzed and retained after quality control 2764 new human ChIP-seq and 208 ChIP-exo datasets available from public sources. The updated human atlas totalize 5798 datasets covering a total of 1135 transcriptional regulators (TRs) with a catalog of 165 million (M) peaks. This ReMap update comes with two unique Arabidopsis regulatory catalogs. First, a catalog of 372 Arabidopsis TRs across 2.6M peaks as a result of the integration of 509 ChIP-seq and DAP-seq datasets. Second, a catalog of 33 histone modifications and variants across 4.5M peaks from the integration of 286 ChIP-seq datasets. All catalogs are made available through track hubs at Ensembl and UCSC Genome Browsers. Additionally, this update comes with a new web framework providing an interactive user-interface, including improved search features. Finally, full programmatically access to the underlying data is available using a RESTful API together with a new R Shiny interface for a TRs binding enrichment analysis tool.