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Navigating the ENCODE Encyclopedia: Exploring Candidate Regulatory Elements, Linked Genes, and Genetic Variation with SCREEN

ENCODE Workshop - October 2017, ASHG

Monitor with a double helixOn October 17, 2017, the ENCODE Consortium held a workshop at the American Society of Human Genetics (ASHG) annual meeting.

This advanced workshop began with an overview of the ENCODE project. The contents and underlying methods of the human and mouse ENCODE Registry of candidate Regulatory Elements (cRE) followed. Next was a live demo of Search Candidate Regulatory Elements by ENCODE (SCREEN), an online tool that enables users to explore cREs across hundreds of human and mouse cell and tissue types and filter regions by various facets.

Participants used SCREEN to work through hands-on examples focusing on comparing enhancer-like elements across tissues, predicting enhancer-gene interactions, and annotating genetic variants.

Exercises demonstrated how to access and download supporting data, how to visualize regions of interest using dynamic graphs and external genome browsers, and how to compare gene expression profiles, intersect regions and correlate signals for datasets of interest with the ENCODE Encyclopedia.

Workshop attendees received instruction or hands-on experience on the following resources:

  • Using the ENCODE portal [encodeproject.org]
  • The ENCODE Registry of Candidate Regulatory Elements (cRE)
  • Using SCREEN to query ENCODE and REMC data
  • ENCODE Use Cases
  • Exercises using SCREEN

This workshop educated researchers, clinicians and genetic counselors on how to use ENCODE data to further biological investigation.

Note: All slides and handouts are in PDF format.

  • Agenda

  • ENCODE Overview
    Zhiping Weng, University of Massachusetts Medical School

    Video - Slides
  • ENCODE Registry of Candidate Regulatory Elements (cRE)
    Jill Moore, University of Massachusetts Medical School

    Video - Slides
  • SCREEN Demonstration
    Michael Pucaro, University of Massachusetts Medical School

    Video
  • Use Cases for SCREEN
    Jill Moore, University of Massachusetts Medical School

    Video - Slides
  • Exercises Using SCREEN
    Jill Moore, University of Massachusetts Medical School

    Video - Handouts
  • Solutions to Exercises Using SCREEN
    Jill Moore, University of Massachusetts Medical School

    VideoHandouts

 

For questions or more information contact:

Zhiping Weng, Ph.D.
E-mail: zhipingweng@gmail.com

 

Posted: March 28, 2018