TY - JOUR
T1 - An integrated encyclopedia of DNA elements in the human genome
AU - Principal investigators (steering committee)
AU - Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis)
AU - Broad Institute Group (data production and analysis)
AU - Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis)
AU - Data coordination center at UC Santa Cruz (production data coordination)
AU - Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis)
AU - Genome Institute of Singapore group (data production and analysis)
AU - HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis)
AU - Lawrence Berkeley National Laboratory group (targeted experimental validation)
AU - NHGRI groups (data production and analysis)
AU - Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis)
AU - Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis)
AU - University of Albany SUNY group (data production and analysis)
AU - University of Chicago Stanford group (data production and analysis)
AU - University of Heidelberg group (targeted experimental validation)
AU - University of Massachusetts Medical School Bioinformatics group (data production and analysis)
AU - University of Washington University of Massachusetts Medical Center group (data production and analysis)
AU - Data Analysis Center (data analysis)
AU - The ENCODE Project Consortium
AU - Data production leads (data production)
AU - Lead analysts (data analysis)
AU - Writing group
AU - NHGRI project management (scientific management)
AU - Dunham, Ian
AU - Kundaje, Anshul
AU - Aldred, Shelley F.
AU - Collins, Patrick J.
AU - Davis, Carrie A.
AU - Doyle, Francis
AU - Epstein, Charles B.
AU - Frietze, Seth
AU - Harrow, Jennifer
AU - Kaul, Rajinder
AU - Khatun, Jainab
AU - Lajoie, Bryan R.
AU - Landt, Stephen G.
AU - Lee, Bum Kyu
AU - Pauli, Florencia
AU - Rosenbloom, Kate R.
AU - Sabo, Peter
AU - Safi, Alexias
AU - Sanyal, Amartya
AU - Shoresh, Noam
AU - Simon, Jeremy M.
AU - Song, Lingyun
AU - Trinklein, Nathan D.
AU - Altshuler, Robert C.
AU - Birney, Ewan
AU - Brown, James B.
AU - Cheng, Chao
AU - Djebali, Sarah
AU - Dong, Xianjun
AU - Ernst, Jason
AU - Furey, Terrence S.
AU - Gerstein, Mark
AU - Giardine, Belinda
AU - Greven, Melissa
AU - Hardison, Ross C.
AU - Harris, Robert S.
AU - Herrero, Javier
AU - Hoffman, Michael M.
AU - Iyer, Sowmya
AU - Kellis, Manolis
AU - Kheradpour, Pouya
AU - Lassmann, Timo
AU - Li, Qunhua
AU - Lin, Xinying
AU - Marinov, Georgi K.
AU - Merkel, Angelika
AU - Mortazavi, Ali
AU - Parker, Stephen C.J.
AU - Abyzov, Alexej
AU - Victorsen, Alec
N1 - Funding Information:
Acknowledgements We thank additional members of our laboratories and institutions who have contributed to the experimental and analytical components of this project. We thank D. Leja for assistance with production of the figures. The Consortium is funded by grants from the NHGRI as follows: production grants: U54HG004570 (B. E. Bernstein); U01HG004695 (E. Birney); U54HG004563 (G. E. Crawford); U54HG004557 (T. R. Gingeras); U54HG004555 (T. J. Hubbard); U41HG004568 (W. J. Kent); U54HG004576 (R. M. Myers); U54HG004558 (M. Snyder); U54HG004592 (J. A. Stamatoyannopoulos). Pilot grants: R01HG003143 (J. Dekker); RC2HG005591 and R01HG003700 (M. C. Giddings); R01HG004456-03 (Y. Ruan); U01HG004571 (S. A. Tenenbaum); U01HG004561 (Z. Weng); RC2HG005679 (K. P. White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591, R01HG003541,U01HG004561,RC2HG005679and R01HG003988(L.Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (L. Elnitski, ZIAHG200323; E. H. Margulies, ZIAHG200341). Research in the Pennachio laboratory was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.
PY - 2012/9/6
Y1 - 2012/9/6
N2 - The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.
AB - The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.
UR - http://www.scopus.com/inward/record.url?scp=84865790047&partnerID=8YFLogxK
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U2 - 10.1038/nature11247
DO - 10.1038/nature11247
M3 - Article
C2 - 22955616
AN - SCOPUS:84865790047
SN - 0028-0836
VL - 489
SP - 57
EP - 74
JO - Nature
JF - Nature
IS - 7414
ER -