Ensembl 2014

被引:1038
作者
Flicek, Paul [1 ,2 ]
Amode, M. Ridwan [2 ]
Barrell, Daniel [2 ]
Beal, Kathryn [1 ]
Billis, Konstantinos [2 ]
Brent, Simon [2 ]
Carvalho-Silva, Denise [1 ]
Clapham, Peter [2 ]
Coates, Guy [2 ]
Fitzgerald, Stephen [1 ]
Gil, Laurent [1 ]
Giron, Carlos Garcia [2 ]
Gordon, Leo [1 ]
Hourlier, Thibaut [2 ]
Hunt, Sarah [1 ]
Johnson, Nathan [1 ]
Juettemann, Thomas [1 ]
Kaehaeri, Andreas K. [2 ]
Keenan, Stephen [1 ]
Kulesha, Eugene [1 ]
Martin, Fergal J. [2 ]
Maurel, Thomas [1 ]
McLaren, William M. [1 ]
Murphy, Daniel N. [2 ]
Nag, Rishi [2 ]
Overduin, Bert [1 ]
Pignatelli, Miguel [1 ]
Pritchard, Bethan [2 ]
Pritchard, Emily [1 ]
Riat, Harpreet S. [2 ]
Ruffier, Magali [1 ]
Sheppard, Daniel [2 ]
Taylor, Kieron [1 ]
Thormann, Anja [1 ]
Trevanion, Stephen J. [2 ]
Vullo, Alessandro [1 ]
Wilder, Steven P. [1 ]
Wilson, Mark [2 ]
Zadissa, Amonida [1 ]
Aken, Bronwen L. [2 ]
Birney, Ewan [1 ]
Cunningham, Fiona [1 ]
Harrow, Jennifer [2 ]
Herrero, Javier [1 ]
Hubbard, Tim J. P. [2 ]
Kinsella, Rhoda [1 ]
Muffato, Matthieu [1 ]
Parker, Anne [2 ]
Spudich, Giulietta [1 ]
Yates, Andy [1 ]
机构
[1] European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England
[2] 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;
关键词
GENOME; DATABASE; UNIFICATION; VARIANTS; RESOURCE; ONTOLOGY; SEQUENCE; BROWSER; TOOL;
D O I
10.1093/nar/gkt1196
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
Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.
引用
收藏
页码:D749 / D755
页数:7
相关论文
共 44 条
[1]   An integrated map of genetic variation from 1,092 human genomes [J].
Altshuler, David M. ;
Durbin, Richard M. ;
Abecasis, Goncalo R. ;
Bentley, David R. ;
Chakravarti, Aravinda ;
Clark, Andrew G. ;
Donnelly, Peter ;
Eichler, Evan E. ;
Flicek, Paul ;
Gabriel, Stacey B. ;
Gibbs, Richard A. ;
Green, Eric D. ;
Hurles, Matthew E. ;
Knoppers, Bartha M. ;
Korbel, Jan O. ;
Lander, Eric S. ;
Lee, Charles ;
Lehrach, Hans ;
Mardis, Elaine R. ;
Marth, Gabor T. ;
McVean, Gil A. ;
Nickerson, Deborah A. ;
Schmidt, Jeanette P. ;
Sherry, Stephen T. ;
Wang, Jun ;
Wilson, Richard K. ;
Gibbs, Richard A. ;
Dinh, Huyen ;
Kovar, Christie ;
Lee, Sandra ;
Lewis, Lora ;
Muzny, Donna ;
Reid, Jeff ;
Wang, Min ;
Wang, Jun ;
Fang, Xiaodong ;
Guo, Xiaosen ;
Jian, Min ;
Jiang, Hui ;
Jin, Xin ;
Li, Guoqing ;
Li, Jingxiang ;
Li, Yingrui ;
Li, Zhuo ;
Liu, Xiao ;
Lu, Yao ;
Ma, Xuedi ;
Su, Zhe ;
Tai, Shuaishuai ;
Tang, Meifang .
NATURE, 2012, 491 (7422) :56-65
[2]   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
[3]   Update on activities at the Universal Protein Resource (UniProt) in 2013 [J].
Apweiler, Rolf ;
Martin, Maria Jesus ;
O'Donovan, Claire ;
Magrane, Michele ;
Alam-Faruque, Yasmin ;
Alpi, Emanuela ;
Antunes, Ricardo ;
Arganiska, Joanna ;
Casanova, Elisabet Barrera ;
Bely, Benoit ;
Bingley, Mark ;
Bonilla, Carlos ;
Britto, Ramona ;
Bursteinas, Borisas ;
Chan, Wei Mun ;
Chavali, Gayatri ;
Cibrian-Uhalte, Elena ;
Da Silva, Alan ;
De Giorgi, Maurizio ;
Dimmer, Emily ;
Fazzini, Francesco ;
Gane, Paul ;
Fedotov, Alexander ;
Castro, Leyla Garcia ;
Garmiri, Penelope ;
Hatton-Ellis, Emma ;
Hieta, Reija ;
Huntley, Rachael ;
Jacobsen, Julius ;
Jones, Rachel ;
Legge, Duncan ;
Liu, Wudong ;
Luo, Jie ;
MacDougall, Alistair ;
Mutowo, Prudence ;
Nightingale, Andrew ;
Orchard, Sandra ;
Patient, Samuel ;
Pichler, Klemens ;
Poggioli, Diego ;
Pundir, Sangya ;
Pureza, Luis ;
Qi, Guoying ;
Rosanoff, Steven ;
Sawford, Tony ;
Sehra, Harminder ;
Turner, Edward ;
Volynkin, Vladimir ;
Wardell, Tony ;
Watkins, Xavier .
NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D43-D47
[4]   Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[5]   The NIH Roadmap Epigenomics Mapping Consortium [J].
Bernstein, Bradley E. ;
Stamatoyannopoulos, John A. ;
Costello, Joseph F. ;
Ren, Bing ;
Milosavljevic, Aleksandar ;
Meissner, Alexander ;
Kellis, Manolis ;
Marra, Marco A. ;
Beaudet, Arthur L. ;
Ecker, Joseph R. ;
Farnham, Peggy J. ;
Hirst, Martin ;
Lander, Eric S. ;
Mikkelsen, Tarjei S. ;
Thomson, James A. .
NATURE BIOTECHNOLOGY, 2010, 28 (10) :1045-1048
[6]   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)
[7]   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
[8]   An integrated encyclopedia of DNA elements in the human genome [J].
Dunham, Ian ;
Kundaje, Anshul ;
Aldred, Shelley F. ;
Collins, Patrick J. ;
Davis, CarrieA. ;
Doyle, Francis ;
Epstein, Charles B. ;
Frietze, Seth ;
Harrow, Jennifer ;
Kaul, Rajinder ;
Khatun, Jainab ;
Lajoie, Bryan R. ;
Landt, Stephen G. ;
Lee, Bum-Kyu ;
Pauli, Florencia ;
Rosenbloom, Kate R. ;
Sabo, Peter ;
Safi, Alexias ;
Sanyal, Amartya ;
Shoresh, Noam ;
Simon, Jeremy M. ;
Song, Lingyun ;
Trinklein, Nathan D. ;
Altshuler, Robert C. ;
Birney, Ewan ;
Brown, James B. ;
Cheng, Chao ;
Djebali, Sarah ;
Dong, Xianjun ;
Dunham, Ian ;
Ernst, Jason ;
Furey, Terrence S. ;
Gerstein, Mark ;
Giardine, Belinda ;
Greven, Melissa ;
Hardison, Ross C. ;
Harris, Robert S. ;
Herrero, Javier ;
Hoffman, Michael M. ;
Iyer, Sowmya ;
Kellis, Manolis ;
Khatun, Jainab ;
Kheradpour, Pouya ;
Kundaje, Anshul ;
Lassmann, Timo ;
Li, Qunhua ;
Lin, Xinying ;
Marinov, Georgi K. ;
Merkel, Angelika ;
Mortazavi, Ali .
NATURE, 2012, 489 (7414) :57-74
[9]   The Sequence Ontology: a tool for the unification of genome annotations [J].
Eilbeck, K ;
Lewis, SE ;
Mungall, CJ ;
Yandell, M ;
Stein, L ;
Durbin, R ;
Ashburner, M .
GENOME BIOLOGY, 2005, 6 (05)
[10]   Ensembl 2013 [J].
Flicek, Paul ;
Ahmed, Ikhlak ;
Amode, M. Ridwan ;
Barrell, Daniel ;
Beal, Kathryn ;
Brent, Simon ;
Carvalho-Silva, Denise ;
Clapham, Peter ;
Coates, Guy ;
Fairley, Susan ;
Fitzgerald, Stephen ;
Gil, Laurent ;
Garcia-Giron, Carlos ;
Gordon, Leo ;
Hourlier, Thibaut ;
Hunt, Sarah ;
Juettemann, Thomas ;
Kaehaeri, Andreas K. ;
Keenan, Stephen ;
Komorowska, Monika ;
Kulesha, Eugene ;
Longden, Ian ;
Maurel, Thomas ;
McLaren, William M. ;
Muffato, Matthieu ;
Nag, Rishi ;
Overduin, Bert ;
Pignatelli, Miguel ;
Pritchard, Bethan ;
Pritchard, Emily ;
Riat, Harpreet Singh ;
Ritchie, Graham R. S. ;
Ruffier, Magali ;
Schuster, Michael ;
Sheppard, Daniel ;
Sobral, Daniel ;
Taylor, Kieron ;
Thormann, Anja ;
Trevanion, Stephen ;
White, Simon ;
Wilder, Steven P. ;
Aken, Bronwen L. ;
Birney, Ewan ;
Cunningham, Fiona ;
Dunham, Ian ;
Harrow, Jennifer ;
Herrero, Javier ;
Hubbard, Tim J. P. ;
Johnson, Nathan ;
Kinsella, Rhoda .
NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D48-D55