Learn about The ENCODE Project , (ENCyclopedia of DNA Elements), an international consortium of researchers who are moving beyond the basic information of the reference genome sequence. Researchers are using many cutting-edge technologies to learn as much as possible about variations, genes, non-coding transcripts, regulatory elements, and genome structure and more, in extensive detail across the entire genome. The ENCODE project is coordinated by the NHGRI. The UCSC Genome Browser is the designated Data Coordination Center (DCC) , for the ENCODE project, and the official ENCODE data repository. In this tutorial we examine aspects of the ENCODE project and data types, and explore ways for you to access and learn about the ENCODE data available under the UCSC Genome Browser. This tutorial assumes the user has familiarity with the software functionality of the UCSC Genome Browser as described in the Introductory and Advanced Topics tutorials. The focus of this material is on the human ENCODE data at this time. If you are interested in the fly and worm aspects of the project, please visit the modENCODE site for these model organisms.

Note: A second tutorial goes beyond these foundations and explores ways to interact with ENCODE data in 2012. See ENCODE Data Available through the UCSC Genome Browser

You will learn:

  • The foundations and background of the ENCODE project
  • Key differences between the pilot phase and the current production phase
  • To identify ENCODE data in the UCSC Genome Browser, and explore the data use policies
  • What types of data are available under ENCODE, and where to find details of the data types and technologies
  • How to interact with the data in the graphical browser, table browser, and by downloading


This tutorial is a part of the tutorial group Human variations. You might find the other tutorials in the group interesting:

GAD: Genetic Association Database: An archived database associating human genes and polymorphisms with diseases

Madeline 2.0: Human pedigree diagram tools

DrugBank: A chemoinformatics and bioinformatics resource

DGV: Database of Genomic Variants: Database of Genomic Variants, DGV, catalogs and displays structural variation in the human genome

NIEHS SNPs: National Institute for Environmental Health Sciences Environmental Genome Project (EGP) SNPs

OMIM: Online Mendelian Inheritance in Man (OMIM): A database of human genes, genetic diseases and disorders

CGAP: Characterize the molecular genetic changes that cause a normal cell to become a cancer cell

HapMap: HapMap, a database and analysis resource of human variation

Genetics Home Reference: A collection of data describing the effects of genetic variability on human health and disease

GeneSNPs: An integrated view of gene structure and SNP variations

dbGaP: A database of genotypes and phenotypes with extensive variation data and clinical details

SeattleSNPs: Human SNPs in genes

dbSNP: NCBI's SNP database

GeneTests: GeneTests, a current, comprehensive genetic testing resource

This tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:

UCSC Genome Browser: The Additional Tools: Additional tools at the UCSC Genome Browser

UCSC Genome Browser: Custom Tracks and Table Browser: UCSC Genome Browser advanced topics

UCSC Archaeal Genome Browser: Provides you with many research and analysis tools that can be used to examine the genomes of more than 50 microbial species from the domain archaea.


UCSC Genome Browser: An Introduction: The UCSC Genome Browser Introduction


Genome Databases (euk) : Genomic databases or repositories primarily aimed at eukaryotic organisms. Some may contain prokaryotic data as well.


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Tip of the Week: Gemini, exploration of genetic variation: You Tube: This week's tip of the week is on Gemini which is the acronym for "GENome MINing." Unlike most of the tips we give every week, this one is a software package. But, it is does use and integra...

Spanking #ENCODE: While I was on the road last week--ironically to do workshops including one on ENCODE data in the UCSC Genome Browser, a conflama erupted over a new paper that was published essentially spanking the EN...

Updated ENCODE tutorial and training materials from OpenHelix once again freely available.: OpenHelix and the UCSC Bioinformatics group have worked together to give everyone free access to the newly updated ENCODE tutorial until the end of February 2013. The online tutorial suite teaches user...

New ENCODE track data available: On Friday I caught this announcement from the ENCODE mailing list. Fresh new data for your mining pleasure! Histone Modifications by ChIP-seq from ENCODE/University of Washington This track shows ge...


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