Ensembl 2011

被引:534
作者
Flicek, Paul [1 ,2 ]
Amode, M. Ridwan [2 ]
Barrell, Daniel [2 ]
Beal, Kathryn [1 ]
Brent, Simon [2 ]
Chen, Yuan [1 ]
Clapham, Peter [2 ]
Coates, Guy [2 ]
Fairley, Susan [2 ]
Fitzgerald, Stephen [1 ]
Gordon, Leo [1 ]
Hendrix, Maurice [2 ]
Hourlier, Thibaut [2 ]
Johnson, Nathan [1 ]
Kaehaeri, Andreas [1 ]
Keefe, Damian [1 ]
Keenan, Stephen [1 ]
Kinsella, Rhoda [1 ]
Kokocinski, Felix [2 ]
Kulesha, Eugene [1 ]
Larsson, Pontus [1 ]
Longden, Ian [1 ]
McLaren, William [1 ]
Overduin, Bert [1 ]
Pritchard, Bethan [2 ]
Riat, Harpreet Singh [2 ]
Rios, Daniel [1 ]
Ritchie, Graham R. S. [1 ]
Ruffier, Magali [2 ]
Schuster, Michael [1 ]
Sobral, Daniel [1 ]
Spudich, Giulietta [1 ]
Tang, Y. Amy [2 ]
Trevanion, Stephen [2 ]
Vandrovcova, Jana [1 ]
Vilella, Albert J. [1 ]
White, Simon [2 ]
Wilder, Steven P. [1 ]
Zadissa, Amonida [2 ]
Zamora, Jorge [1 ]
Aken, Bronwen L. [2 ]
Birney, Ewan [1 ]
Cunningham, Fiona [1 ]
Dunham, Ian [1 ]
Durbin, Richard [2 ]
Fernandez-Suarez, Xose M. [1 ]
Herrero, Javier [1 ]
Hubbard, Tim J. P. [2 ]
Parker, Anne [2 ]
Proctor, Glenn [1 ]
机构
[1] Wellcome Trust Genome Campus, European Bioinformat Inst, Cambridge CB10 1SD, England
[2] Wellcome Trust Genome Campus, Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England
基金
英国生物技术与生命科学研究理事会; 英国惠康基金; 美国国家卫生研究院;
关键词
GENOME; DATABASE; RESOURCE;
D O I
10.1093/nar/gkq1064
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 Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.
引用
收藏
页码:D800 / D806
页数:7
相关论文
共 31 条
[1]  
[Anonymous], GENETIC VARIATION LA
[2]   The Universal Protein Resource (UniProt) in 2010 [J].
Apweiler, Rolf ;
Martin, Maria Jesus ;
O'Donovan, Claire ;
Magrane, Michele ;
Alam-Faruque, Yasmin ;
Antunes, Ricardo ;
Barrell, Daniel ;
Bely, Benoit ;
Bingley, Mark ;
Binns, David ;
Bower, Lawrence ;
Browne, Paul ;
Chan, Wei Mun ;
Dimmer, Emily ;
Eberhardt, Ruth ;
Fedotov, Alexander ;
Foulger, Rebecca ;
Garavelli, John ;
Huntley, Rachael ;
Jacobsen, Julius ;
Kleen, Michael ;
Laiho, Kati ;
Leinonen, Rasko ;
Legge, Duncan ;
Lin, Quan ;
Liu, Wudong ;
Luo, Jie ;
Orchard, Sandra ;
Patient, Samuel ;
Poggioli, Diego ;
Pruess, Manuela ;
Corbett, Matt ;
di Martino, Giuseppe ;
Donnelly, Mike ;
van Rensburg, Pieter ;
Bairoch, Amos ;
Bougueleret, Lydie ;
Xenarios, Ioannis ;
Altairac, Severine ;
Auchincloss, Andrea ;
Argoud-Puy, Ghislaine ;
Axelsen, Kristian ;
Baratin, Delphine ;
Blatter, Marie-Claude ;
Boeckmann, Brigitte ;
Bolleman, Jerven ;
Bollondi, Laurent ;
Boutet, Emmanuel ;
Quintaje, Silvia Braconi ;
Breuza, Lionel .
NUCLEIC ACIDS RESEARCH, 2010, 38 :D142-D148
[3]   Consistent annotation of gene expression arrays [J].
Ballester, Benoit ;
Johnson, Nathan ;
Proctor, Glenn ;
Flicek, Paul .
BMC GENOMICS, 2010, 11
[4]   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
[5]   The HGNC Database in 2008: a resource for the human genome [J].
Bruford, Elspeth A. ;
Lush, Michael J. ;
Wright, Mathew W. ;
Sneddon, Tam P. ;
Povey, Sue ;
Birney, Ewan .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D445-D448
[6]   Ensembl variation resources [J].
Chen, Yuan ;
Cunningham, Fiona ;
Rios, Daniel ;
McLaren, William M. ;
Smith, James ;
Pritchard, Bethan ;
Spudich, Giulietta M. ;
Brent, Simon ;
Kulesha, Eugene ;
Marin-Garcia, Pablo ;
Smedley, Damian ;
Birney, Ewan ;
Flicek, Paul .
BMC GENOMICS, 2010, 11
[7]   Public data archives for genomic structural variation [J].
Church, Deanna M. ;
Lappalainen, Ilkka ;
Sneddon, Tam P. ;
Hinton, Jonathan ;
Maguire, Michael ;
Lopez, John ;
Garner, John ;
Paschall, Justin ;
DiCuccio, Michael ;
Yaschenko, Eugene ;
Scherer, Stephen W. ;
Feuk, Lars ;
Flicek, Paul .
NATURE GENETICS, 2010, 42 (10) :813-814
[8]  
Cooper D.N., 2006, CURR PROTOC BIOINFOR, V21, P1131
[9]   Distribution and intensity of constraint in mammalian genomic sequence [J].
Cooper, GM ;
Stone, EA ;
Asimenos, G ;
Green, ED ;
Batzoglou, S ;
Sidow, A .
GENOME RESEARCH, 2005, 15 (07) :901-913
[10]   Locus Reference Genomic sequences: an improved basis for describing human DNA variants [J].
Dalgleish, Raymond ;
Flicek, Paul ;
Cunningham, Fiona ;
Astashyn, Alex ;
Tully, Raymond E. ;
Proctor, Glenn ;
Chen, Yuan ;
McLaren, William M. ;
Larsson, Pontus ;
Vaughan, Brendan W. ;
Beroud, Christophe ;
Dobson, Glen ;
Lehvaeslaiho, Heikki ;
Taschner, Peter E. M. ;
den Dunnen, Johan T. ;
Devereau, Andrew ;
Birney, Ewan ;
Brookes, Anthony J. ;
Maglott, Donna R. .
GENOME MEDICINE, 2010, 2