ENCODE whole-genome data in the UCSC Genome Browser

被引：174

作者：

Rosenbloom, Kate R. ^{[1
]}

Dreszer, Timothy R. ^{[1
]}

Pheasant, Michael ^{[1
,2
]}

Barber, Galt P. ^{[1
]}

Meyer, Laurence R. ^{[1
]}

Pohl, Andy ^{[1
]}

Raney, Brian J. ^{[1
]}

Wang, Ting ^{[3
]}

Hinrichs, Angie S. ^{[1
]}

Zweig, Ann S. ^{[1
]}

Fujita, Pauline A. ^{[1
]}

Learned, Katrina ^{[1
]}

Rhead, Brooke ^{[1
]}

Smith, Kayla E. ^{[1
]}

Kuhn, Robert M. ^{[1
]}

Karolchik, Donna ^{[1
]}

Haussler, David ^{[1
,4
]}

Kent, W. James ^{[1
]}

机构：

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

[2] Queensland Facil Adv Bioinformat, Brisbane, Qld 4072, Australia

[3] Washington Univ, Ctr Genome Sci, Dept Genet, St Louis, MO 63108 USA

[4] Univ Calif Santa Cruz, Howard Hughes Med Inst, Santa Cruz, CA 95064 USA

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷

关键词：

PROJECT; ELEMENTS;

D O I：

10.1093/nar/gkp961

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 Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements. The ENCODE Data Coordination Center at The University of California, Santa Cruz (UCSC) is the primary repository for experimental results generated by ENCODE investigators. These results are captured in the UCSC Genome Bioinformatics database and download server for visualization and data mining via the UCSC Genome Browser and companion tools (Rhead et al. The UCSC Genome Browser Database: update 2010, in this issue). The ENCODE web portal at UCSC (http://encodeproject.org or http://genome.ucsc.edu/ENCODE) provides information about the ENCODE data and convenient links for access.

引用

页码：D620 / D625

页数：6

共 8 条

[1] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[2] Unlocking the secrets of the genome [J].

Celniker, Susan E. ;

Dillon, Laura A. L. ;

Gerstein, Mark B. ;

Gunsalus, Kristin C. ;

Henikoff, Steven ;

Karpen, Gary H. ;

Kellis, Manolis ;

Lai, Eric C. ;

Lieb, Jason D. ;

MacAlpine, David M. ;

Micklem, Gos ;

Piano, Fabio ;

Snyder, Michael ;

Stein, Lincoln ;

White, Kevin P. ;

Waterston, Robert H. .

NATURE, 2009, 459 (7249) :927-930

[3] 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

[4] The human genome browser at UCSC [J].

Kent, WJ ;

Sugnet, CW ;

Furey, TS ;

Roskin, KM ;

Pringle, TH ;

Zahler, AM ;

Haussler, D .

GENOME RESEARCH, 2002, 12 (06) :996-1006

[5] The UCSC Genome Browser Database: update 2009 [J].

Kuhn, R. M. ;

Karolchik, D. ;

Zweig, A. S. ;

Wang, T. ;

Smith, K. E. ;

Rosenbloom, K. R. ;

Rhead, B. ;

Raney, B. J. ;

Pohl, A. ;

Pheasant, M. ;

Meyer, L. ;

Hsu, F. ;

Hinrichs, A. S. ;

Harte, R. A. ;

Giardine, B. ;

Fujita, P. ;

Diekhans, M. ;

Dreszer, T. ;

Clawson, H. ;

Barber, G. P. ;

Haussler, D. ;

Kent, W. J. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D755-D761

[6] The Sequence Alignment/Map format and SAMtools [J].

Li, Heng ;

Handsaker, Bob ;

Wysoker, Alec ;

Fennell, Tim ;

Ruan, Jue ;

Homer, Nils ;

Marth, Gabor ;

Abecasis, Goncalo ;

Durbin, Richard .

BIOINFORMATICS, 2009, 25 (16) :2078-2079

[7] The ENCODE project at UC Santa Cruz [J].

Thomas, Daryl J. ;

Rosenbloom, Kate R. ;

Clawson, Hiram ;

Hinrichs, Angie S. ;

Trumbower, Heather ;

Raney, Brian J. ;

Karolchik, Donna ;

Barber, Galt P. ;

Harte, Rachel A. ;

Hillman-Jackson, Jennifer ;

Kuhn, Robert M. ;

Rhead, Brooke L. ;

Smith, Kayla E. ;

Thakkapallayil, Archana ;

Zweig, Ann S. ;

Haussler, David ;

Kent, W. James .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D663-D667

[8] ENCODE: More genomic empowerment [J].

Weinstock, George M. .

GENOME RESEARCH, 2007, 17 (06) :667-668

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