ENCODE Data at UCSC
Tutorial and training materials by OpenHelix
| 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. We’ll 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. We’ll 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 consortium’s 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. | Advertisement:
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You'll 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
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Related tutorialsThis tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:
| Recent BioMed Central research articles citing this resourceWang Guohua et al., Identification of regulatory regions of bidirectional genes in cervical cancer Proceedings of the 2011 International Conference on Bioinformatics and Computational Biology (BIOCOMP"11) The 2011 International Conference on Bioinformatics and Computational Biology (BIOCOMP"11). BMC Medical Genomics (2013) doi:10.1186/1755-8794-6-S1-S5 Patnala Radhika et al., Candidate gene association studies: a comprehensive guide to useful in silico tools Statistical and computational genetics. BMC Genetics (2013) doi:10.1186/1471-2156-14-39 Qian Maoxiang et al., Structurally differentiated cis -elements that interact with PU.1 are functionally distinguishable in acute promyelocytic leukemia. Journal of Hematology Oncology (2013) doi:10.1186/1756-8722-6-25 Tomescu I Alexandru et al., A novel min-cost flow method for estimating transcript expression with RNA-Seq Proceedings of the Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2013) RECOMB-seq: Third Annual Recomb Satellite Workshop on Massively Parallel Sequencing. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-S5-S15 Poptsova Maria et al., Impact of constitutional copy number variants on biological pathway evolution Genome evolution and evolutionary systems biology. BMC Evolutionary Biology (2013) doi:10.1186/1471-2148-13-19 |
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