Ensembl 2011

被引:536
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
美国国家卫生研究院; 英国生物技术与生命科学研究理事会; 英国惠康基金;
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
[21]   JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles [J].
Portales-Casamar, Elodie ;
Thongjuea, Supat ;
Kwon, Andrew T. ;
Arenillas, David ;
Zhao, Xiaobei ;
Valen, Eivind ;
Yusuf, Dimas ;
Lenhard, Boris ;
Wasserman, Wyeth W. ;
Sandelin, Albin .
NUCLEIC ACIDS RESEARCH, 2010, 38 :D105-D110
[22]   The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes [J].
Pruitt, Kim D. ;
Harrow, Jennifer ;
Harte, Rachel A. ;
Wallin, Craig ;
Diekhans, Mark ;
Maglott, Donna R. ;
Searle, Steve ;
Farrell, Catherine M. ;
Loveland, Jane E. ;
Ruef, Barbara J. ;
Hart, Elizabeth ;
Suner, Marie-Marthe ;
Landrum, Melissa J. ;
Aken, Bronwen ;
Ayling, Sarah ;
Baertsch, Robert ;
Fernandez-Banet, Julio ;
Cherry, Joshua L. ;
Curwen, Val ;
DiCuccio, Michael ;
Kellis, Manolis ;
Lee, Jennifer ;
Lin, Michael F. ;
Schuster, Michael ;
Shkeda, Andrew ;
Amid, Clara ;
Brown, Garth ;
Dukhanina, Oksana ;
Frankish, Adam ;
Hart, Jennifer ;
Maidak, Bonnie L. ;
Mudge, Jonathan ;
Murphy, Michael R. ;
Murphy, Terence ;
Rajan, Jeena ;
Rajput, Bhanu ;
Riddick, Lillian D. ;
Snow, Catherine ;
Steward, Charles ;
Webb, David ;
Weber, Janet A. ;
Wilming, Laurens ;
Wu, Wenyu ;
Birney, Ewan ;
Haussler, David ;
Hubbard, Tim ;
Ostell, James ;
Durbin, Richard ;
Lipman, David .
GENOME RESEARCH, 2009, 19 (07) :1316-1323
[23]   A database and API for variation, dense genotyping and resequencing data [J].
Rios, Daniel ;
McLaren, William M. ;
Chen, Yuan ;
Birney, Ewan ;
Stabenau, Arne ;
Flicek, Paul ;
Cunningham, Fiona .
BMC BIOINFORMATICS, 2010, 11
[24]   ENCODE whole-genome data in the UCSC Genome Browser [J].
Rosenbloom, Kate R. ;
Dreszer, Timothy R. ;
Pheasant, Michael ;
Barber, Galt P. ;
Meyer, Laurence R. ;
Pohl, Andy ;
Raney, Brian J. ;
Wang, Ting ;
Hinrichs, Angie S. ;
Zweig, Ann S. ;
Fujita, Pauline A. ;
Learned, Katrina ;
Rhead, Brooke ;
Smith, Kayla E. ;
Kuhn, Robert M. ;
Karolchik, Donna ;
Haussler, David ;
Kent, W. James .
NUCLEIC ACIDS RESEARCH, 2010, 38 :D620-D625
[25]   eHive: An Artificial Intelligence workflow system for genomic analysis [J].
Severin, Jessica ;
Beal, Kathryn ;
Vilella, Albert J. ;
Fitzgerald, Stephen ;
Schuster, Michael ;
Gordon, Leo ;
Ureta-Vidal, Abel ;
Flicek, Paul ;
Herrero, Javier .
BMC BIOINFORMATICS, 2010, 11
[26]   BioMart - biological queries made easy [J].
Smedley, Damian ;
Haider, Syed ;
Ballester, Benoit ;
Holland, Richard ;
London, Darin ;
Thorisson, Gudmundur ;
Kasprzyk, Arek .
BMC GENOMICS, 2009, 10
[27]   The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes [J].
Sprague, Judy ;
Bayraktaroglu, Leyla ;
Bradford, Yvonne ;
Conlin, Tom ;
Dunn, Nathan ;
Fashena, David ;
Frazer, Ken ;
Haendel, Melissa ;
Howe, Douglas G. ;
Knight, Jonathan ;
Mani, Prita ;
Moxon, Sierra A. T. ;
Pich, Christian ;
Ramachandran, Sridhar ;
Schaper, Kevin ;
Segerdell, Erik ;
Shao, Xiang ;
Singer, Amy ;
Song, Peiran ;
Sprunger, Brock ;
Van Slyke, Ceri E. ;
Westerfield, Monte .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D768-D772
[28]   Touring Ensembl: A practical guide to genome browsing [J].
Spudich, Giulietta M. ;
Fernandez-Suarez, Xose M. .
BMC GENOMICS, 2010, 11
[29]   The ensembl core software libraries [J].
Stabenau, A ;
McVicker, G ;
Melsopp, C ;
Proctor, G ;
Clamp, M ;
Birney, E .
GENOME RESEARCH, 2004, 14 (05) :929-933
[30]   EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates [J].
Vilella, Albert J. ;
Severin, Jessica ;
Ureta-Vidal, Abel ;
Heng, Li ;
Durbin, Richard ;
Birney, Ewan .
GENOME RESEARCH, 2009, 19 (02) :327-335