Ensembl 2013

被引:779
作者
Flicek, Paul [1 ,2 ]
Ahmed, Ikhlak [1 ]
Amode, M. Ridwan [2 ]
Barrell, Daniel [2 ]
Beal, Kathryn [1 ]
Brent, Simon [2 ]
Carvalho-Silva, Denise [1 ]
Clapham, Peter [2 ]
Coates, Guy [2 ]
Fairley, Susan [2 ]
Fitzgerald, Stephen [1 ]
Gil, Laurent [1 ]
Garcia-Giron, Carlos [2 ]
Gordon, Leo [1 ]
Hourlier, Thibaut [2 ]
Hunt, Sarah [1 ]
Juettemann, Thomas [1 ]
Kaehaeri, Andreas K. [2 ]
Keenan, Stephen [1 ]
Komorowska, Monika [1 ]
Kulesha, Eugene [1 ]
Longden, Ian [1 ]
Maurel, Thomas [1 ]
McLaren, William M. [1 ]
Muffato, Matthieu [1 ]
Nag, Rishi [2 ]
Overduin, Bert [1 ]
Pignatelli, Miguel [1 ]
Pritchard, Bethan [2 ]
Pritchard, Emily [1 ]
Riat, Harpreet Singh [2 ]
Ritchie, Graham R. S. [1 ]
Ruffier, Magali [1 ]
Schuster, Michael [1 ]
Sheppard, Daniel [2 ]
Sobral, Daniel [1 ]
Taylor, Kieron [1 ]
Thormann, Anja [1 ]
Trevanion, Stephen [2 ]
White, Simon [2 ]
Wilder, Steven P. [1 ]
Aken, Bronwen L. [2 ]
Birney, Ewan [1 ]
Cunningham, Fiona [1 ]
Dunham, Ian [1 ]
Harrow, Jennifer [2 ]
Herrero, Javier [1 ]
Hubbard, Tim J. P. [2 ]
Johnson, Nathan [1 ]
Kinsella, Rhoda [1 ]
机构
[1] European Bioinformat Inst, Cambridge CB10 1SD, England
[2] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England
基金
英国惠康基金; 英国生物技术与生命科学研究理事会;
关键词
DATABASE; DISCOVERY; TOOL; EVOLUTION; SEQUENCES; VARIANTS; DISEASES; BROWSER; SYSTEM;
D O I
10.1093/nar/gks1236
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) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.
引用
收藏
页码:D48 / D55
页数:8
相关论文
共 46 条
[1]   BLUEPRINT to decode the epigenetic signature written in blood [J].
Adams, David ;
Altucci, Lucia ;
Antonarakis, Stylianos E. ;
Ballesteros, Juan ;
Beck, Stephan ;
Bird, Adrian ;
Bock, Christoph ;
Boehm, Bernhard ;
Campo, Elias ;
Caricasole, Andrea ;
Dahl, Fredrik ;
Dermitzakis, Emmanouil T. ;
Enver, Tariq ;
Esteller, Manel ;
Estivill, Xavier ;
Ferguson-Smith, Anne ;
Fitzgibbon, Jude ;
Flicek, Paul ;
Giehl, Claudia ;
Graf, Thomas ;
Grosveld, Frank ;
Guigo, Roderic ;
Gut, Ivo ;
Helin, Kristian ;
Jarvius, Jonas ;
Kueppers, Ralf ;
Lehrach, Hans ;
Lengauer, Thomas ;
Lernmark, Ake ;
Leslie, David ;
Loeffler, Markus ;
Macintyre, Elizabeth ;
Mai, Antonello ;
Martens, Joost H. A. ;
Minucci, Saverio ;
Ouwehand, Willem H. ;
Pelicci, Pier Giuseppe ;
Pendeville, Helene ;
Porse, Bo ;
Rakyan, Vardhman ;
Reik, Wolf ;
Schrappe, Martin ;
Schuebeler, Dirk ;
Seifert, Martin ;
Siebert, Reiner ;
Simmons, David ;
Soranzo, Nicole ;
Spicuglia, Salvatore ;
Stratton, Michael ;
Stunnenberg, Hendrik G. .
NATURE BIOTECHNOLOGY, 2012, 30 (03) :224-226
[2]   A method and server for predicting damaging missense mutations [J].
Adzhubei, Ivan A. ;
Schmidt, Steffen ;
Peshkin, Leonid ;
Ramensky, Vasily E. ;
Gerasimova, Anna ;
Bork, Peer ;
Kondrashov, Alexey S. ;
Sunyaev, Shamil R. .
NATURE METHODS, 2010, 7 (04) :248-249
[3]   A map of human genome variation from population-scale sequencing [J].
Altshuler, David ;
Durbin, Richard M. ;
Abecasis, Goncalo R. ;
Bentley, David R. ;
Chakravarti, Aravinda ;
Clark, Andrew G. ;
Collins, Francis S. ;
De la Vega, Francisco M. ;
Donnelly, Peter ;
Egholm, Michael ;
Flicek, Paul ;
Gabriel, Stacey B. ;
Gibbs, Richard A. ;
Knoppers, Bartha M. ;
Lander, Eric S. ;
Lehrach, Hans ;
Mardis, Elaine R. ;
McVean, Gil A. ;
Nickerson, DebbieA. ;
Peltonen, Leena ;
Schafer, Alan J. ;
Sherry, Stephen T. ;
Wang, Jun ;
Wilson, Richard K. ;
Gibbs, Richard A. ;
Deiros, David ;
Metzker, Mike ;
Muzny, Donna ;
Reid, Jeff ;
Wheeler, David ;
Wang, Jun ;
Li, Jingxiang ;
Jian, Min ;
Li, Guoqing ;
Li, Ruiqiang ;
Liang, Huiqing ;
Tian, Geng ;
Wang, Bo ;
Wang, Jian ;
Wang, Wei ;
Yang, Huanming ;
Zhang, Xiuqing ;
Zheng, Huisong ;
Lander, Eric S. ;
Altshuler, David L. ;
Ambrogio, Lauren ;
Bloom, Toby ;
Cibulskis, Kristian ;
Fennell, Tim J. ;
Gabriel, Stacey B. .
NATURE, 2010, 467 (7319) :1061-1073
[4]   A New Face and New Challenges for Online Mendelian Inheritance in Man (OMIM®) [J].
Amberger, Joanna ;
Bocchini, Carol ;
Hamosh, Ada .
HUMAN MUTATION, 2011, 32 (05) :564-567
[5]   Major submissions tool developments at the European nucleotide archive [J].
Amid, Clara ;
Birney, Ewan ;
Bower, Lawrence ;
Cerdeno-Tarraga, Ana ;
Cheng, Ying ;
Cleland, Iain ;
Faruque, Nadeem ;
Gibson, Richard ;
Goodgame, Neil ;
Hunter, Christopher ;
Jang, Mikyung ;
Leinonen, Rasko ;
Liu, Xin ;
Oisel, Arnaud ;
Pakseresht, Nima ;
Plaister, Sheila ;
Radhakrishnan, Rajesh ;
Reddy, Kethi ;
Riviere, Stephane ;
Rossello, Marc ;
Senf, Alexander ;
Smirnov, Dimitriy ;
Ten Hoopen, Petra ;
Vaughan, Daniel ;
Vaughan, Robert ;
Zalunin, Vadim ;
Cochrane, Guy .
NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D43-D47
[6]  
[Anonymous], GENETIC VARIATION LA
[7]   Reorganizing the protein space at the Universal Protein Resource (UniProt) [J].
Apweiler, Rolf ;
Martin, Maria Jesus ;
O'Donovan, Claire ;
Magrane, Michele ;
Alam-Faruque, Yasmin ;
Antunes, Ricardo ;
Casanova, Elisabet Barrera ;
Bely, Benoit ;
Bingley, Mark ;
Bower, Lawrence ;
Bursteinas, Borisas ;
Chan, Wei Mun ;
Chavali, Gayatri ;
Da Silva, Alan ;
Dimmer, Emily ;
Eberhardt, Ruth ;
Fazzini, Francesco ;
Fedotov, Alexander ;
Garavelli, John ;
Castro, Leyla Garcia ;
Gardner, Michael ;
Hieta, Reija ;
Huntley, Rachael ;
Jacobsen, Julius ;
Legge, Duncan ;
Liu, Wudong ;
Luo, Jie ;
Orchard, Sandra ;
Patient, Samuel ;
Pichler, Klemens ;
Poggioli, Diego ;
Pontikos, Nikolas ;
Pundir, Sangya ;
Rosanoff, Steven ;
Sawford, Tony ;
Sehra, Harminder ;
Turner, Edward ;
Wardell, Tony ;
Watkins, Xavier ;
Corbett, Matt ;
Donnelly, Mike ;
van Rensburg, Pieter ;
Goujon, Mickael ;
McWilliam, Hamish ;
Lopez, Rodrigo ;
Xenarios, Ioannis ;
Bougueleret, Lydie ;
Bridge, Alan ;
Poux, Sylvain ;
Redaschi, Nicole .
NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D71-D75
[8]   The evolution of gene expression levels in mammalian organs [J].
Brawand, David ;
Soumillon, Magali ;
Necsulea, Anamaria ;
Julien, Philippe ;
Csardi, Gabor ;
Harrigan, Patrick ;
Weier, Manuela ;
Liechti, Angelica ;
Aximu-Petri, Ayinuer ;
Kircher, Martin ;
Albert, Frank W. ;
Zeller, Ulrich ;
Khaitovich, Philipp ;
Gruetzner, Frank ;
Bergmann, Sven ;
Nielsen, Rasmus ;
Paeaebo, Svante ;
Kaessmann, Henrik .
NATURE, 2011, 478 (7369) :343-+
[9]   Modernizing Reference Genome Assemblies [J].
Church, Deanna M. ;
Schneider, Valerie A. ;
Graves, Tina ;
Auger, Katherine ;
Cunningham, Fiona ;
Bouk, Nathan ;
Chen, Hsiu-Chuan ;
Agarwala, Richa ;
McLaren, William M. ;
Ritchie, Graham R. S. ;
Albracht, Derek ;
Kremitzki, Milinn ;
Rock, Susan ;
Kotkiewicz, Holland ;
Kremitzki, Colin ;
Wollam, Aye ;
Trani, Lee ;
Fulton, Lucinda ;
Fulton, Robert ;
Matthews, Lucy ;
Whitehead, Siobhan ;
Chow, Will ;
Torrance, James ;
Dunn, Matthew ;
Harden, Glenn ;
Threadgold, Glen ;
Wood, Jonathan ;
Collins, Joanna ;
Heath, Paul ;
Griffiths, Guy ;
Pelan, Sarah ;
Grafham, Darren ;
Eichler, Evan E. ;
Weinstock, George ;
Mardis, Elaine R. ;
Wilson, Richard K. ;
Howe, Kerstin ;
Flicek, Paul ;
Hubbard, Tim .
PLOS BIOLOGY, 2011, 9 (07)
[10]   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