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. 2019 Dec;68(1):e89.
doi: 10.1002/cpbi.89.

The ENCODE Portal as an Epigenomics Resource

Affiliations

The ENCODE Portal as an Epigenomics Resource

Jennifer Jou et al. Curr Protoc Bioinformatics. 2019 Dec.

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.

Keywords: ENCODE; database; epigenetics; human genome; regulatory elements.

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Figures

Figure 1
Figure 1
The ENCODE home page. This image shows the Data drop‐down menu in the toolbar opened. The first item in the menu is a link to the Experiment Matrix page.
Figure 2
Figure 2
The Experiment Matrix page displays available ENCODE data in a matrix with biosample types and assays as the axes. Each cell of the matrix is clickable and leads to a list of experiments matching the given combination of biosample type and assay.
Figure 3
Figure 3
The Experiment search page displays ENCODE data as a list of search results. Each experiment is shown with a brief summary of the biological material and assay name, and a link to its individual experiment summary page with more metadata details (see Fig. 5). On the left is the facet sidebar, which can be used to modify and refine the search results. The “Add all items to cart” button is a Cart function, explained further in Support Protocol 3.
Figure 4
Figure 4
A truncated view of the facets with the items that should be selected after step 13 of the Basic Protocol.
Figure 5
Figure 5
An experiment summary page. Below the page title and audits, the page is organized into distinct sections containing the following information: (A) Summary section: key info including but not limited to the assay performed, biosample used, assay target if applicable, platform, and controls. (B) Attribution section: information about the lab that performed the experiment and when the experiment was released. (C) Replicates section: table of experimental replicates with links to biosamples, antibodies, libraries, and genetic modifications when applicable. (D) Files section: information about the raw and processed data files generated from this experiment and subsequent analysis, provenance of data files as reflected in file association graph, and visualization of experiment‐specific genome tracks when applicable. (E) Documents section: links to additional protocol documents describing the experimental methods.
Figure 6
Figure 6
The Cart page. On the left are the file selectors. Although visually similar to the facet sidebar explored in the Basic Protocol, these file selectors only affect which files will be included in files.txt, introduced in Support Protocol 1. As selections are made, the number above the selectors, which reads “137 files selected” in this figure, will update dynamically. On the right is the list of experiments saved in the cart.
Figure 7
Figure 7
Genome browser tab in the Files section of an Experiment summary page. This tab contains the embedded Valis genome browser, which can be used to visualize signal and peaks tracks directly on the ENCODE portal. Filters to the left of the browser are used to select which tracks to visualize. Here, only the “signal p‐value” tracks are selected for visualization. The small arrow above the words “Choose an assembly” can be used to collapse and expand the filter sidebar.

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References

Literature Cited

    1. Aken, B. L. , Achuthan, P. , Akanni, W. , Amode, M. R. , Bernsdorff, F. , Bhai, J. , … Flicek, P. (2017). Ensembl 2017. Nucleic Acids Research, 45(D1), D635–D642. doi: 10.1093/nar/gkw1104. - DOI - PMC - PubMed
    1. Barrett, T. , Wilhite, S. E. , Ledoux, P. , Evangelista, C. , Kim, I. F. , Tomashevsky, M. , … Soboleva, A. (2013). NCBI GEO: Archive for functional genomics data sets: Update. Nucleic Acids Research, 41(Database issue), D991–D995. doi: 10.1093/nar/gks1193. - DOI - PMC - PubMed
    1. Bujold, D. , Morais, D. A. L. , Gauthier, C. , Côté, C. , Caron, M. , Kwan, T. , … Bourque, G. (2016). The international human epigenome consortium data portal. Cell Systems, 3(5), 496–499.e2. doi: 10.1016/j.cels.2016.10.019. - DOI - PubMed
    1. Davis, C. A. , Hitz, B. C. , Sloan, C. A. , Chan, E. T. , Davidson, J. M. , Gabdank, I. , … Cherry, J. M. (2018). The encyclopedia of DNA elements (ENCODE): Data portal update. Nucleic Acids Research, 46(D1), D794–D801. doi: 10.1093/nar/gkx1081. - DOI - PMC - PubMed
    1. Durand, N. C. , Robinson, J. T. , Shamim, M. S. , Machol, I. , Mesirov, J. P. , Lander, E. S. , & Aiden, E. L. (2016). Juicebox provides a visualization system for Hi‐C contact maps with unlimited zoom. Cell Systems, 3(1), 99–101. doi: 10.1016/j.cels.2015.07.012. - DOI - PMC - PubMed

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