ENCODE data at the ENCODE portal

Cricket A. Sloan; Esther T. Chan; Jean M. Davidson; Venkat S. Malladi; J. Seth Strattan; Benjamin C. Hitz; Idan Gabdank; Aditi K. Narayanan; Marcus Ho; Brian T. Lee; Laurence D. Rowe; Timothy R. Dreszer; Greg Roe; Nikhil R. Podduturi; Forrest Tanaka; Eurie L. Hong; J. Michael Cherry

doi:10.1093/nar/gkv1160

ENCODE data at the ENCODE portal

Cricket A. Sloan, Esther T. Chan, Jean M. Davidson, Venkat S. Malladi, J. Seth Strattan, Benjamin C. Hitz, Idan Gabdank, Aditi K. Narayanan, Marcus Ho, Brian T. Lee, Laurence D. Rowe, Timothy R. Dreszer, Greg Roe, Nikhil R. Podduturi, Forrest Tanaka, Eurie L. Hong, J. Michael Cherry

Research output: Contribution to journal › Article › peer-review

327 Scopus citations

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.

Original language	English (US)
Pages (from-to)	D726-D732
Journal	Nucleic acids research
Volume	44
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkv1160
State	Published - 2016
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkv1160

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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.",

author = "Sloan, {Cricket A.} and Chan, {Esther T.} and Davidson, {Jean M.} and Malladi, {Venkat S.} and Strattan, {J. Seth} and Hitz, {Benjamin C.} and Idan Gabdank and Narayanan, {Aditi K.} and Marcus Ho and Lee, {Brian T.} and Rowe, {Laurence D.} and Dreszer, {Timothy R.} and Greg Roe and Podduturi, {Nikhil R.} and Forrest Tanaka and Hong, {Eurie L.} and Cherry, {J. Michael}",

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year = "2016",

doi = "10.1093/nar/gkv1160",

language = "English (US)",

volume = "44",

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AU - Sloan, Cricket A.

AU - Chan, Esther T.

AU - Davidson, Jean M.

AU - Malladi, Venkat S.

AU - Strattan, J. Seth

AU - Hitz, Benjamin C.

AU - Gabdank, Idan

AU - Narayanan, Aditi K.

AU - Ho, Marcus

AU - Lee, Brian T.

AU - Rowe, Laurence D.

AU - Dreszer, Timothy R.

AU - Roe, Greg

AU - Podduturi, Nikhil R.

AU - Tanaka, Forrest

AU - Hong, Eurie L.

AU - Cherry, J. Michael

PY - 2016

Y1 - 2016

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ENCODE data at the ENCODE portal

Abstract

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