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Trends Genet. 2016 Apr;32(4):238-249. doi: 10.1016/j.tig.2016.02.002. Epub 2016 Mar 5.

Deciphering ENCODE.

Author information

1
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
2
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor MI 48109, USA. Electronic address: apboyle@umich.edu.

Abstract

The ENCODE project represents a major leap from merely describing and comparing genomic sequences to surveying them for direct indicators of function. The astounding quantity of data produced by the ENCODE consortium can serve as a map to locate specific landmarks, guide hypothesis generation, and lead us to principles and mechanisms underlying genome biology. Despite its broad appeal, the size and complexity of the repository can be intimidating to prospective users. We present here some background about the ENCODE data, survey the resources available for accessing them, and describe a few simple principles to help prospective users choose the data type(s) that best suit their needs, where to get them, and how to use them to their best advantage.

KEYWORDS:

ChIP-seq; DNase-seq; ENCODE; RNA-seq; gene regulation; genomics

PMID:
26962025
DOI:
10.1016/j.tig.2016.02.002
[Indexed for MEDLINE]

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