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A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

The ENCODE Project Consortium *

PLoS Biology

Public Library of Science

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      Abstract

      The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

      Author Summary

      The Encyclopedia of DNA Elements (ENCODE) Project was created to enable the scientific and medical communities to interpret the human genome sequence and to use it to understand human biology and improve health. The ENCODE Consortium, a large group of scientists from around the world, uses a variety of experimental methods to identify and describe the regions of the 3 billion base-pair human genome that are important for function. Using experimental, computational, and statistical analyses, we aimed to discover and describe genes, transcripts, and transcriptional regulatory regions, as well as DNA binding proteins that interact with regulatory regions in the genome, including transcription factors, different versions of histones and other markers, and DNA methylation patterns that define states of the genome in various cell types. The ENCODE Project has developed standards for each experiment type to ensure high-quality, reproducible data and novel algorithms to facilitate analysis. All data and derived results are made available through a freely accessible database. This article provides an overview of the complete project and the resources it is generating, as well as examples to illustrate the application of ENCODE data as a user's guide to facilitate the interpretation of the human genome.

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      Most cited references 123

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      We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41-52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3' untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices.
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            Author and article information

            Affiliations
            Adolf Butenandt Institute, Germany
            Contributors
            Role: Academic Editor
            Journal
            PLoS Biol
            plos
            plosbiol
            PLoS Biology
            Public Library of Science (San Francisco, USA )
            1544-9173
            1545-7885
            April 2011
            April 2011
            19 April 2011
            : 9
            : 4
            3079585
            21526222
            PBIOLOGY-D-10-00316
            10.1371/journal.pbio.1001046
            (Academic Editor)
            The ENCODE Project Consortium. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
            Counts
            Pages: 21
            Categories
            Research Article
            Biology
            Computational Biology
            Genetics
            Genomics
            ScienceOpen disciplines:

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