Ensembl 2014

被引:1030
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
    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
    [J]. NATURE, 2012, 491 (7422) : 56 - 65
  • [2] A New Face and New Challenges for Online Mendelian Inheritance in Man (OMIM®)
    Amberger, Joanna
    Bocchini, Carol
    Hamosh, Ada
    [J]. HUMAN MUTATION, 2011, 32 (05) : 564 - 567
  • [3] Update on activities at the Universal Protein Resource (UniProt) in 2013
    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
    [J]. NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) : D43 - D47
  • [4] Gene Ontology: tool for the unification of biology
    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
    [J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
  • [5] The NIH Roadmap Epigenomics Mapping Consortium
    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.
    [J]. NATURE BIOTECHNOLOGY, 2010, 28 (10) : 1045 - 1048
  • [6] Modernizing Reference Genome Assemblies
    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
    [J]. PLOS BIOLOGY, 2011, 9 (07)
  • [7] Distribution and intensity of constraint in mammalian genomic sequence
    Cooper, GM
    Stone, EA
    Asimenos, G
    Green, ED
    Batzoglou, S
    Sidow, A
    [J]. GENOME RESEARCH, 2005, 15 (07) : 901 - 913
  • [8] An integrated encyclopedia of DNA elements in the human genome
    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
    [J]. NATURE, 2012, 489 (7414) : 57 - 74
  • [9] The Sequence Ontology: a tool for the unification of genome annotations
    Eilbeck, K
    Lewis, SE
    Mungall, CJ
    Yandell, M
    Stein, L
    Durbin, R
    Ashburner, M
    [J]. GENOME BIOLOGY, 2005, 6 (05)
  • [10] Ensembl 2013
    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
    [J]. NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) : D48 - D55