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 journalArticle

122 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)D726-D732
JournalNucleic acids research
Volume44
Issue numberD1
DOIs
StatePublished - Jan 1 2016
Externally publishedYes

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Encyclopedias
DNA
RNA Probes
DNA Probes
Human Genome
DNA Methylation
Hypersensitivity
RNA
Population

ASJC Scopus subject areas

  • Genetics

Cite this

Sloan, C. A., Chan, E. T., Davidson, J. M., Malladi, V. S., Strattan, J. S., Hitz, B. C., ... Cherry, J. M. (2016). ENCODE data at the ENCODE portal. Nucleic acids research, 44(D1), D726-D732. https://doi.org/10.1093/nar/gkv1160

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

In: Nucleic acids research, Vol. 44, No. D1, 01.01.2016, p. D726-D732.

Research output: Contribution to journalArticle

Sloan, CA, Chan, ET, Davidson, JM, Malladi, VS, Strattan, JS, Hitz, BC, Gabdank, I, Narayanan, AK, Ho, M, Lee, BT, Rowe, LD, Dreszer, TR, Roe, G, Podduturi, NR, Tanaka, F, Hong, EL & Cherry, JM 2016, 'ENCODE data at the ENCODE portal', Nucleic acids research, vol. 44, no. D1, pp. D726-D732. https://doi.org/10.1093/nar/gkv1160
Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC et al. ENCODE data at the ENCODE portal. Nucleic acids research. 2016 Jan 1;44(D1):D726-D732. https://doi.org/10.1093/nar/gkv1160
Sloan, Cricket A. ; Chan, Esther T. ; Davidson, Jean M. ; Malladi, Venkat S. ; Strattan, J. Seth ; Hitz, Benjamin C. ; Gabdank, Idan ; Narayanan, Aditi K. ; Ho, Marcus ; Lee, Brian T. ; Rowe, Laurence D. ; Dreszer, Timothy R. ; Roe, Greg ; Podduturi, Nikhil R. ; Tanaka, Forrest ; Hong, Eurie L. ; Cherry, J. Michael. / ENCODE data at the ENCODE portal. In: Nucleic acids research. 2016 ; Vol. 44, No. D1. pp. D726-D732.
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