The ENCODE Portal as an Epigenomics Resource

Q1 Biochemistry, Genetics and Molecular Biology

Current protocols in bioinformatics Pub Date : 2019-11-21 DOI:10.1002/cpbi.89

Jennifer Jou, Idan Gabdank, Yunhai Luo, Khine Lin, Paul Sud, Zachary Myers, Jason A. Hilton, Meenakshi S. Kagda, Bonita Lam, Emma O'Neill, Philip Adenekan, Keenan Graham, Ulugbek K. Baymuradov, Stuart R. Miyasato, J. Seth Strattan, Otto Jolanki, Jin-Wook Lee, Casey Litton, Forrest Y. Tanaka, Benjamin C. Hitz, J. Michael Cherry

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引用次数: 19

Abstract

The Encyclopedia of DNA Elements (ENCODE) web portal hosts genomic data generated by the ENCODE Consortium, Genomics of Gene Regulation, The NIH Roadmap Epigenomics Consortium, and the modENCODE and modERN projects. The goal of the ENCODE project is to build a comprehensive map of the functional elements of the human and mouse genomes. Currently, the portal database stores over 500 TB of raw and processed data from over 15,000 experiments spanning assays that measure gene expression, DNA accessibility, DNA and RNA binding, DNA methylation, and 3D chromatin structure across numerous cell lines, tissue types, and differentiation states with selected genetic and molecular perturbations. The ENCODE portal provides unrestricted access to the aforementioned data and relevant metadata as a service to the scientific community. The metadata model captures the details of the experiments, raw and processed data files, and processing pipelines in human and machine-readable form and enables the user to search for specific data either using a web browser or programmatically via REST API. Furthermore, ENCODE data can be freely visualized or downloaded for additional analyses. © 2019 The Authors.

Basic Protocol: Query the portal

Support Protocol 1: Batch downloading

Support Protocol 2: Using the cart to download files

Support Protocol 3: Visualize data

Alternate Protocol: Query building and programmatic access

Abstract Image

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ENCODE门户作为表观基因组学资源

DNA元素百科全书(ENCODE)门户网站承载了ENCODE联盟、基因调控基因组学、NIH路线图表观基因组学联盟以及modENCODE和modERN项目生成的基因组数据。ENCODE计划的目标是建立人类和小鼠基因组功能元素的综合图谱。目前，门户数据库存储了超过500 TB的原始和处理数据，这些数据来自超过15,000个实验，涵盖了测量基因表达、DNA可及性、DNA和RNA结合、DNA甲基化和3D染色质结构的分析，这些分析跨越了许多细胞系、组织类型和具有选定遗传和分子扰动的分化状态。ENCODE门户提供对上述数据和相关元数据的无限制访问，作为对科学界的服务。元数据模型以人类和机器可读的形式捕获实验的细节、原始和处理过的数据文件以及处理管道，并使用户能够使用web浏览器或通过REST API以编程方式搜索特定数据。此外，ENCODE数据可以自由地可视化或下载以进行额外的分析。©2019作者。基本协议:查询portal支持协议1:批量下载支持协议2:使用购物车下载文件支持协议3:可视化数据备用协议:查询构建和程序化访问

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Current protocols in bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry

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