title: ENCODE data at the ENCODE portal.
abstract: The Encyclopedia of DNA Elements (ENCODE) Project is in its third phase of creating a comprehensive catalog of functional elements in the human genome. This phase of the project includes an expansion of assays that measure diverse RNA populations, identify proteins that interact with RNA and DNA, probe regions of DNA hypersensitivity, and measure levels of DNA methylation in a wide range of cell and tissue types to identify putative regulatory elements. To date, results for almost 5000 experiments have been released for use by the scientific community. These data are available for searching, visualization and download at the new ENCODE Portal (www.encodeproject.org). The revamped ENCODE Portal provides new ways to browse and search the ENCODE data based on the metadata that describe the assays as well as summaries of the assays that focus on data provenance. In addition, it is a flexible platform that allows integration of genomic data from multiple projects. The portal experience was designed to improve access to ENCODE data by relying on metadata that allow reusability and reproducibility of the experiments.
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Cricket A
authors.initials: CA
authors.lastname: Sloan
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Esther T
authors.identifier: http://orcid.org/0000-0002-2406-2623
authors.initials: ET
authors.lastname: Chan
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Jean M
authors.identifier: http://orcid.org/0000-0001-5951-5955
authors.initials: JM
authors.lastname: Davidson
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Venkat S
authors.initials: VS
authors.lastname: Malladi
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: J Seth
authors.identifier: http://orcid.org/0000-0002-0144-0564
authors.initials: JS
authors.lastname: Strattan
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Benjamin C
authors.identifier: http://orcid.org/0000-0001-5094-282X
authors.initials: BC
authors.lastname: Hitz
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Idan
authors.identifier: http://orcid.org/0000-0003-3361-3594
authors.initials: I
authors.lastname: Gabdank
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Aditi K
authors.identifier: http://orcid.org/0000-0001-5025-5886
authors.initials: AK
authors.lastname: Narayanan
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Marcus
authors.identifier: http://orcid.org/0000-0003-0627-1859
authors.initials: M
authors.lastname: Ho
authors.affiliation: University of California at Santa Cruz, Center for Biomolecular Science and Engineering, Santa Cruz, CA, 95064, USA.
authors.forename: Brian T
authors.identifier: http://orcid.org/0000-0002-5819-8342
authors.initials: BT
authors.lastname: Lee
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Laurence D
authors.identifier: http://orcid.org/0000-0001-6382-9738
authors.initials: LD
authors.lastname: Rowe
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Timothy R
authors.identifier: http://orcid.org/0000-0002-1420-0754
authors.initials: TR
authors.lastname: Dreszer
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Greg
authors.identifier: http://orcid.org/0000-0002-7328-1283
authors.initials: G
authors.lastname: Roe
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Nikhil R
authors.identifier: http://orcid.org/0000-0002-2592-2090
authors.initials: NR
authors.lastname: Podduturi
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Forrest
authors.identifier: http://orcid.org/0000-0002-8649-6611
authors.initials: F
authors.lastname: Tanaka
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA.
authors.forename: Eurie L
authors.identifier: http://orcid.org/0000-0002-1775-4998
authors.initials: EL
authors.lastname: Hong
authors.affiliation: Stanford University School of Medicine, Department of Genetics, Stanford, CA, 94305, USA cherry@stanford.edu.
authors.forename: J Michael
authors.identifier: http://orcid.org/0000-0001-9163-5180
authors.initials: JM
authors.lastname: Cherry
mesh_terms: D000818:Animals; D004247:DNA / Q000378:metabolism; D030541:Databases, Genetic; D005796:Genes; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D051379:Mice; D011506:Proteins / Q000378:metabolism; D012313:RNA / Q000378:metabolism
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA