ENCODE (Encyclopedia Of DNA Elements) is a big data consortium project that has for years generated huge amounts of important new data and analyses about various structural features and other aspects of genome organization. In this tutorial we will focus on the human and mouse data flowing into the UCSC Genome Browser via the Data Coordination Center (DCC) during the production phase of the project. Well describe the ENCODE portal that provides access to many project topics, and then move to exploring numerous data types in the Genome Browser. We will emphasize how to identify and locate data relevant to your research, and explore the data in the browser and other UCSC interfaces. Well examine visualization strategies and important track control features and track details. This tutorial assumes that the viewer has foundational knowledge of the UCSC Genome Browser and Table Browser tools. We also encourage viewers to access the consortiums publication: The ENCODE Project Consortium (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 9(4): e1001046. doi:10.1371/journal.pbio.1001046.

New: Explore the massive publication collection available on September 5 2012 via the ENCODE Explorer at Nature.

You will learn:

  • Aspects of ENCODE project organization
  • Where to access the ENCODE portal for key project documentation and data collections
  • Ways to find data of interest for your research
  • To visualize and explore ENCODE project results
  • Alternative ways to query or download the data


This tutorial is a part of the tutorial group Advanced Analysis and Queries. You might find the other tutorials in the group interesting:

BioMart: Management and querying of many types of biological data

UniProt: UniProt, Universal Protein Resource

DBTSS: Database of Transcriptional Start Sites

Galaxy: Analysis tools for researchers

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

ENCODE Foundations: ENCyclopedia of DNA Elements

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.


Video Tip of the Week: UCSC features for ENCODE data utilization: As noted in last week's tip about the ENCODE DCC at Stanford, there was a workshop recently for the ENCODE project. There were a lot of folks speaking and a big room full of attendees. You should check...

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VideoTip of the Week: ENCODE @ Ensembl: We have a lot of tutorials (2 in fact, ENCODE Foundations & ENCODE @ UCSC), tips and information about ENCODE. We also have a lot of tutorials (again 2, Ensembl and Ensembl Legacy- on the older versio...

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...


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