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

被引：959

作者：

Myers, Richard M.

Stamatoyannopoulos, John ^{[2
]}

Snyder, Michael ^{[3
]}

Dunham, Ian ^{[4
]}

Hardison, Ross C. ^{[5
]}

Bernstein, Bradley E. ^{[6
]}

Gingeras, Thomas R. ^{[8
]}

Kent, W. James

Birney, Ewan ^{[4
]}

Wold, Barbara ^{[10
]}

Crawford, Gregory E. ^{[12
]}

Bernstein, Bradley E. ^{[6
]}

Epstein, Charles B. ^{[6
]}

Shoresh, Noam ^{[6
]}

Ernst, Jason ^{[6
]}

Mikkelsen, Tarjei S. ^{[6
]}

Kheradpour, Pouya ^{[6
]}

Zhang, Xiaolan ^{[6
]}

Wang, Li ^{[6
]}

Issner, Robbyn ^{[6
]}

Coyne, Michael J. ^{[6
]}

Durham, Timothy ^{[6
]}

Ku, Manching ^{[6
]}

Thanh Truong

Ward, Lucas D. ^{[6
]}

Altshuler, Robert C.

Lin, Michael F. ^{[6
]}

Kellis, Manolis ^{[6
]}

Gingeras, Thomas R. ^{[8
]}

Davis, Carrie A. ^{[8
]}

Kapranov, Philipp ^{[13
]}

Dobin, Alexander ^{[8
]}

Zaleski, Christopher ^{[8
]}

Schlesinger, Felix ^{[8
]}

Batut, Philippe ^{[8
]}

Chakrabortty, Sudipto ^{[8
]}

Jha, Sonali ^{[8
]}

Lin, Wei ^{[8
]}

Drenkow, Jorg ^{[8
]}

Wang, Huaien ^{[8
]}

Bell, Kim ^{[8
]}

Gao, Hui ^{[14
]}

Bell, Ian ^{[13
]}

Dumais, Erica ^{[13
]}

Dumais, Jacqueline ^{[13
]}

Antonarakis, Stylianos E. ^{[15
]}

Ucla, Catherine ^{[15
]}

Borel, Christelle ^{[15
]}

Guigo, Roderic ^{[16
]}

Djebali, Sarah

机构：

[1] HudsonAlpha Inst Biotechnol, Huntsville, AL USA

[2] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[3] Stanford Univ, Sch Med, Dept Genet, Stanford, CA 94305 USA

[4] European Bioinformat Inst EBI, Cambridge, England

[5] Penn State Univ, Dept Biochem & Mol Biol, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA

[6] Broad Inst MT & Harvard, Cambridge, MA USA

[7] Harvard Univ, Sch Med, Boston, MA USA

[8] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[9] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA

[10] CALTECH, Div Biol, Pasadena, CA 91125 USA

[11] CALTECH, Beckman Inst, Pasadena, CA 91125 USA

[12] Duke Univ, Inst Genome Sci & Policy, Durham, NC USA

[13] Affymetrix, Santa Clara, CA USA

[14] Karolinska Inst, Huddinge, Sweden

[15] Univ Geneva, Geneva, Switzerland

[16] Ctr Regulacio Genom, Barcelona, Spain

[17] RIKEN Yokohama Inst, Omics Sci Ctr, Kanagawa, Japan

[18] Cold Spring Harbor Lab, Howard Hughes Med Inst, Cold Spring Harbor, NY 11724 USA

[19] Univ Lausanne, Ctr Integrat Genom, Lausanne, Switzerland

[20] Univ Texas Austin, Sect Mol Genet & Microbiol, Inst Cellular & Mol Biol, Ctr Syst & Synthet Biol, Austin, TX 78712 USA

[21] Univ N Carolina, Carolina Ctr Genome Sci, Dept Biol, Chapel Hill, NC USA

[22] Univ N Carolina, Lineberger Comprehens Canc Ctr, Chapel Hill, NC USA

[23] CALTECH, Ctr Adv Comp Res, Pasadena, CA 91125 USA

[24] Stanford Univ, Sch Med, Dept Pathol, Stanford, CA 94305 USA

[25] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA

[26] NHGRI, Div Intramural Res, NIH, Bethesda, MD 20892 USA

[27] NHGRI, Genome Technol Branch, NIH, Rockville, MD USA

[28] NHGRI, NIH Intramural Sequencing Ctr, NIH, Bethesda, MD 20892 USA

[29] Wellcome Trust Sanger Inst, Hinxton, Cambs, England

[30] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT USA

[31] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT USA

[32] Yale Univ, Dept Comp Sci, New Haven, CT 06520 USA

[33] Ctr Nacl Invest Oncol, Madrid, Spain

[34] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT USA

[35] Yale Univ, Dept Genet, New Haven, CT USA

[36] Univ Massachusetts, Sch Med, Dept Pediat, Worcester, MA USA

[37] Univ So Calif, Norris Comprehens Canc Ctr, Dept Biochem & Mol Biol, Los Angeles, CA USA

[38] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA

[39] Univ Massachusetts, Sch Med, Dept Biochem & Mol Pharmacol, Program Gene Funct & Express, Worcester, MA USA

[40] Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA

[41] Washington Univ, Dept Genet, St Louis, MO 63110 USA

[42] Univ Washington, Dept Comp Sci & Engn, Seattle, WA 98195 USA

[43] Univ Massachusetts, Sch Med, Dept Biochem & Mol Pharmacol, Program Bioinformat & Integrat Biol, Worcester, MA USA

[44] Boston Univ, Bioinformat Program, Boston, MA 02215 USA

[45] SUNY Albany, Coll Nanoscale Sci & Engn, Albany, NY 12222 USA

[46] Childrens Canc Res Inst, Dept Cellular & Struct Biol, San Antonio, TX USA

[47] Boston Univ, Dept Chem, Boston, MA 02215 USA

[48] Boston Univ, Program Bioinformat, Boston, MA 02215 USA

[49] Univ Chicago, Inst Genom & Syst Biol, Chicago, IL 60637 USA

[50] SwitchGear Genom, Menlo Pk, CA USA

来源：

PLOS BIOLOGY | 2011年 / 9卷 / 04期

基金：

美国国家卫生研究院;

关键词：

TRANSCRIPTION FACTOR-BINDING; MESSENGER-RNA SUBSETS; IN-VIVO; COPY-NUMBER; RIBONUCLEOPROTEIN COMPLEXES; CHROMATIN SIGNATURES; METHYLATION PATTERNS; HYPERSENSITIVE SITES; REGULATORY ELEMENTS; STEM-CELLS;

D O I：

10.1371/journal.pbio.1001046

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页数：21

共 121 条

[1] Multiple loci on 8q24 associated with prostate cancer susceptibility [J].

Al Olama, Ali Amin ;

Kote-Jarai, Zsofia ;

Giles, Graham G. ;

Guy, Michelle ;

Morrison, Jonathan ;

Severi, Gianluca ;

Leongamornlert, Daniel A. ;

Tymrakiewicz, Malgorzata ;

Jhavar, Sameer ;

Saunders, Ed ;

Hopper, John L. ;

Southey, Melissa C. ;

Muir, Kenneth R. ;

English, Dallas R. ;

Dearnaley, David P. ;

Ardern-Jones, Audrey T. ;

Hall, Amanda L. ;

O'Brien, Lynne T. ;

Wilkinson, Rosemary A. ;

Sawyer, Emma ;

Lophatananon, Artitaya ;

Horwich, Alan ;

Huddart, Robert A. ;

Khoo, Vincent S. ;

Parker, Christopher C. ;

Woodhouse, Christopher J. ;

Thompson, Alan ;

Christmas, Tim ;

Ogden, Chris ;

Cooper, Colin ;

Donovan, Jenny L. ;

Hamdy, Freddie C. ;

Neal, David E. ;

Eeles, Rosalind A. ;

Easton, Douglas F. .

NATURE GENETICS, 2009, 41 (10) :1058-1060

[2]

[Anonymous], 2006, GENOME BIOL S1

[3]

[Anonymous], 2010, CURR PROTOC MOL BIOL

[4] Widely distributed noncoding purifying selection in the human genome [J].

Asthana, Saurabh ;

Noble, William S. ;

Kryukov, Gregory ;

Grantt, Charles E. ;

Sunyaev, Shamil ;

Stamatoyannopoulos, John A. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (30) :12410-12415

[5] Analysis of sequence conservation at nucleotide resolution [J].

Asthana, Saurabh ;

Roytberg, Mikhail ;

Stamatoyannopoulos, John ;

Sunyaev, Shamil .

PLOS COMPUTATIONAL BIOLOGY, 2007, 3 (12) :2559-2568

[6] Mapping accessible chromatin regions using Sono-Seq [J].

Auerbach, Raymond K. ;

Euskirchen, Ghia ;

Rozowsky, Joel ;

Lamarre-Vincent, Nathan ;

Moqtaderi, Zarmik ;

Lefrancois, Philippe ;

Struhl, Kevin ;

Gerstein, Mark ;

Snyder, Michael .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (35) :14926-14931

[7] The expanding snoRNA world [J].

Bachellerie, JP ;

Cavaillé, J ;

Hüttenhofer, A .

BIOCHIMIE, 2002, 84 (08) :775-790

[8]

Baroni Timothy E., 2008, V419, P93, DOI 10.1007/978-1-59745-033-1_6

[9] High-resolution profiling of histone methylations in the human genome [J].

Barski, Artern ;

Cuddapah, Suresh ;

Cui, Kairong ;

Roh, Tae-Young ;

Schones, Dustin E. ;

Wang, Zhibin ;

Wei, Gang ;

Chepelev, Iouri ;

Zhao, Keji .

CELL, 2007, 129 (04) :823-837

[10] A bivalent chromatin structure marks key developmental genes in embryonic stem cells [J].

Bernstein, BE ;

Mikkelsen, TS ;

Xie, XH ;

Kamal, M ;

Huebert, DJ ;

Cuff, J ;

Fry, B ;

Meissner, A ;

Wernig, M ;

Plath, K ;

Jaenisch, R ;

Wagschal, A ;

Feil, R ;

Schreiber, SL ;

Lander, ES .

CELL, 2006, 125 (02) :315-326

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