An encyclopedia of mouse DNA elements (Mouse ENCODE)

被引：348

作者：

Stamatoyannopoulos, John A. ^{[1
]}

Snyder, Michael ^{[2
]}

Hardison, Ross ^{[3
]}

Ren, Bing ^{[4
]}

Gingeras, Thomas ^{[5
]}

Gilbert, David M.

Groudine, Mark ^{[6
,7
]}

Bender, Michael ^{[7
]}

Kaul, Rajinder ^{[1
]}

Canfield, Theresa ^{[1
]}

Giste, Erica ^{[1
]}

Johnson, Audra ^{[1
]}

Zhang, Mia ^{[7
]}

Balasundaram, Gayathri ^{[7
]}

Byron, Rachel ^{[7
]}

Roach, Vaughan ^{[1
]}

Sabo, Peter J. ^{[1
]}

Sandstrom, Richard ^{[1
]}

Stehling, A. Sandra ^{[1
]}

Thurman, Robert E. ^{[1
]}

Weissman, Sherman M. ^{[8
]}

Cayting, Philip ^{[8
,9
,10
]}

Hariharan, Manoj ^{[2
]}

Lian, Jin ^{[9
]}

Cheng, Yong ^{[2
]}

Landt, Stephen G. ^{[2
]}

Ma, Zhihai ^{[2
]}

Wold, Barbara J. ^{[11
]}

Dekker, Job ^{[12
]}

Crawford, Gregory E. ^{[13
,14
]}

Keller, Cheryl A. ^{[3
]}

Wu, Weisheng ^{[3
]}

Morrissey, Christopher ^{[3
]}

Kumar, Swathi A. ^{[3
]}

Mishra, Tejaswini ^{[3
]}

Jain, Deepti ^{[3
]}

Byrska-Bishop, Marta ^{[3
]}

Blankenberg, Daniel ^{[3
]}

Lajoie, Bryan R. ^{[1
,2
]}

Jain, Gaurav ^{[12
]}

Sanyal, Amartya ^{[12
]}

Chen, Kaun-Bei ^{[13
]}

Denas, Olgert ^{[13
]}

Taylor, James ^{[15
]}

Blobel, Gerd A. ^{[16
]}

Weiss, Mitchell J. ^{[16
]}

Pimkin, Max ^{[16
]}

Deng, Wulan ^{[16
]}

Marinov, Georgi K. ^{[11
]}

Williams, Brian A.

机构：

[1] Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA

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

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

[4] Univ Calif San Diego, Inst Genom Med, Dept Cellular & Mol Med, La Jolla, CA 92093 USA

[5] Cold Spring Harbor Lab, Dept Funct Genom, Cold Spring Harbor, NY 11724 USA

[6] Florida State Univ, Dept Biol Sci, Tallahassee, FL 32306 USA

[7] Fred Hutchinson Canc Res Ctr, Div Basic Sci, Seattle, WA 98104 USA

[8] Yale Univ, Dept Genet, New Haven, CT 06510 USA

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

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

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

[12] Univ Massachusetts, Sch Med, Dept Mol Pharmacol & Biochem, Worcester, MA USA

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

[14] Duke Univ, Dept Pediat, Durham, NC 27706 USA

[15] Emory Univ, Dept Math & Comp Sci, Atlanta, GA 30322 USA

[16] Childrens Hosp Philadelphia, Div Hematol, Abramson Res Ctr, Philadelphia, PA 19104 USA

[17] Univ Calif Irvine, Dept Dev & Cell Biol, Irvine, CA 92717 USA

[18] Ctr Genom Regulat, Div Bioinformat & Genom, Barcelona, Catalunya, Spain

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

[20] NHGRI, NIH, Bethesda, MD 20892 USA

来源：

GENOME BIOLOGY | 2012年 / 13卷 / 08期

关键词：

ENCODE Project; mouse genome; DNasel hypersensitive sites; histone modifications; transcriptome; transcription factor binding sites; comparative genomics; ChIP-seq; RNA-seq; HUMAN-DISEASE; COMPARATIVE GENOMICS; MODELS;

D O I：

10.1186/gb-2012-13-8-418

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.

引用

页数：5

共 22 条

[1] Deletion of ultraconserved elements yields viable mice [J].

Ahituv, Nadav ;

Zhu, Yiwen ;

Visel, Axel ;

Holt, Amy ;

Afzal, Veena ;

Pennacchio, Len A. ;

Rubin, Edward M. .

PLOS BIOLOGY, 2007, 5 (09) :1906-1911

[2] Mouse models of human disease .2. Recent progress and future directions [J].

Bedell, MA ;

Largaespada, DA ;

Jenkins, NA ;

Copeland, NG .

GENES & DEVELOPMENT, 1997, 11 (01) :11-43

[3]

Cheng Jan-Fang, 2007, Methods Mol Biol, V366, P229

[4] The ENCODE (ENCyclopedia of DNA elements) Project [J].

Feingold, EA ;

Good, PJ ;

Guyer, MS ;

Kamholz, S ;

Liefer, L ;

Wetterstrand, K ;

Collins, FS ;

Gingeras, TR ;

Kampa, D ;

Sekinger, EA ;

Cheng, J ;

Hirsch, H ;

Ghosh, S ;

Zhu, Z ;

Pate, S ;

Piccolboni, A ;

Yang, A ;

Tammana, H ;

Bekiranov, S ;

Kapranov, P ;

Harrison, R ;

Church, G ;

Struhl, K ;

Ren, B ;

Kim, TH ;

Barrera, LO ;

Qu, C ;

Van Calcar, S ;

Luna, R ;

Glass, CK ;

Rosenfeld, MG ;

Guigo, R ;

Antonarakis, SE ;

Birney, E ;

Brent, M ;

Pachter, L ;

Reymond, A ;

Dermitzakis, ET ;

Dewey, C ;

Keefe, D ;

Denoeud, F ;

Lagarde, J ;

Ashurst, J ;

Hubbard, T ;

Wesselink, JJ ;

Castelo, R ;

Eyras, E ;

Myers, RM ;

Sidow, A ;

Batzoglou, S .

SCIENCE, 2004, 306 (5696) :636-640

[5] Mouse models for human disease [J].

Hardouin, SN ;

Nagy, A .

CLINICAL GENETICS, 2000, 57 (04) :237-244

[6] Histone modifications at human enhancers reflect global cell-type-specific gene expression [J].

Heintzman, Nathaniel D. ;

Hon, Gary C. ;

Hawkins, R. David ;

Kheradpour, Pouya ;

Stark, Alexander ;

Harp, Lindsey F. ;

Ye, Zhen ;

Lee, Leonard K. ;

Stuart, Rhona K. ;

Ching, Christina W. ;

Ching, Keith A. ;

Antosiewicz-Bourget, Jessica E. ;

Liu, Hui ;

Zhang, Xinmin ;

Green, Roland D. ;

Lobanenkov, Victor V. ;

Stewart, Ron ;

Thomson, James A. ;

Crawford, Gregory E. ;

Kellis, Manolis ;

Ren, Bing .

NATURE, 2009, 459 (7243) :108-112

[7]

Hesselberth JR, 2009, NAT METHODS, V6, P283, DOI [10.1038/NMETH.1313, 10.1038/nmeth.1313]

[8]

Holt BD, 2001, TRENDS CARDIOVAS MED, V11, P82

[9] Chromatin accessibility pre-determines glucocorticoid receptor binding patterns [J].

John, Sam ;

Sabo, Peter J. ;

Thurman, Robert E. ;

Sung, Myong-Hee ;

Biddie, Simon C. ;

Johnson, Thomas A. ;

Hager, Gordon L. ;

Stamatoyannopoulos, John A. .

NATURE GENETICS, 2011, 43 (03) :264-U116

[10] A high-resolution map of human evolutionary constraint using 29 mammals [J].

Lindblad-Toh, Kerstin ;

Garber, Manuel ;

Zuk, Or ;

Lin, Michael F. ;

Parker, Brian J. ;

Washietl, Stefan ;

Kheradpour, Pouya ;

Ernst, Jason ;

Jordan, Gregory ;

Mauceli, Evan ;

Ward, Lucas D. ;

Lowe, Craig B. ;

Holloway, Alisha K. ;

Clamp, Michele ;

Gnerre, Sante ;

Alfoeldi, Jessica ;

Beal, Kathryn ;

Chang, Jean ;

Clawson, Hiram ;

Cuff, James ;

Di Palma, Federica ;

Fitzgerald, Stephen ;

Flicek, Paul ;

Guttman, Mitchell ;

Hubisz, Melissa J. ;

Jaffe, David B. ;

Jungreis, Irwin ;

Kent, W. James ;

Kostka, Dennis ;

Lara, Marcia ;

Martins, Andre L. ;

Massingham, Tim ;

Moltke, Ida ;

Raney, Brian J. ;

Rasmussen, Matthew D. ;

Robinson, Jim ;

Stark, Alexander ;

Vilella, Albert J. ;

Wen, Jiayu ;

Xie, Xiaohui ;

Zody, Michael C. ;

Worley, Kim C. ;

Kovar, Christie L. ;

Muzny, Donna M. ;

Gibbs, Richard A. ;

Warren, Wesley C. ;

Mardis, Elaine R. ;

Weinstock, George M. ;

Wilson, Richard K. ;

Birney, Ewan .

NATURE, 2011, 478 (7370) :476-482

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