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ENCODE whole-genome data in the UCSC Genome Browser: update 2012.

The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of production-level effort generating high-quality whole-genome functional annotations of the human genome. The past year has brought the ENCODE compendium of functional elements to critical mass, with a diverse set of 27 biochemical assays now covering 200 distinct human cell types. Within the mouse genome, which has been under study by ENCODE groups for the past 2 years, 37 cell types have been assayed. Over 2000 individual experiments have been completed and submitted to the Data Coordination Center for public use. UCSC makes this data available on the quality-reviewed public Genome Browser ( and on an early-access Preview Browser ( Visual browsing, data mining and download of raw and processed data files are all supported. An ENCODE portal ( provides specialized tools and information about the ENCODE data sets.

Pubmed ID: 22075998


  • Rosenbloom KR
  • Dreszer TR
  • Long JC
  • Malladi VS
  • Sloan CA
  • Raney BJ
  • Cline MS
  • Karolchik D
  • Barber GP
  • Clawson H
  • Diekhans M
  • Fujita PA
  • Goldman M
  • Gravell RC
  • Harte RA
  • Hinrichs AS
  • Kirkup VM
  • Kuhn RM
  • Learned K
  • Maddren M
  • Meyer LR
  • Pohl A
  • Rhead B
  • Wong MC
  • Zweig AS
  • Haussler D
  • Kent WJ


Nucleic acids research

Publication Data

January 23, 2012

Associated Grants

  • Agency: NHGRI NIH HHS, Id: 3P41HG002371-10S1
  • Agency: NHGRI NIH HHS, Id: 3U41HG004568-03S1
  • Agency: NHGRI NIH HHS, Id: 5P41HG002371-10
  • Agency: NHGRI NIH HHS, Id: 5U41HG004568-04
  • Agency: Howard Hughes Medical Institute, Id:

Mesh Terms

  • Animals
  • Databases, Nucleic Acid
  • Genome
  • Genome, Human
  • Humans
  • Internet
  • Mice
  • Molecular Sequence Annotation
  • Software