Ensembl 2016

被引：1072

作者：

Yates, Andrew ^{[1
]}

Akanni, Wasiu ^{[1
]}

Amode, M. Ridwan ^{[1
]}

Barrell, Daniel ^{[1
]}

Billis, Konstantinos ^{[1
]}

Carvalho-Silva, Denise ^{[1
]}

Cummins, Carla ^{[1
]}

Clapham, Peter ^{[2
]}

Fitzgerald, Stephen ^{[1
]}

Gil, Laurent ^{[1
]}

Giron, Carlos Garcia ^{[1
]}

Gordon, Leo ^{[1
]}

Hourlier, Thibaut ^{[1
]}

Hunt, Sarah E. ^{[1
]}

Janacek, Sophie H. ^{[1
]}

Johnson, Nathan ^{[1
]}

Juettemann, Thomas ^{[1
]}

Keenan, Stephen ^{[1
]}

Lavidas, Ilias ^{[1
]}

Martin, Fergal J. ^{[1
]}

Maurel, Thomas ^{[1
]}

McLaren, William ^{[1
]}

Murphy, Daniel N. ^{[1
]}

Nag, Rishi ^{[1
]}

Nuhn, Michael ^{[1
]}

Parker, Anne ^{[1
]}

Patricio, Mateus ^{[1
]}

Pignatelli, Miguel ^{[1
]}

Rahtz, Matthew ^{[2
]}

Riat, Harpreet Singh ^{[1
]}

Sheppard, Daniel ^{[1
]}

Taylor, Kieron ^{[1
]}

Thormann, Anja ^{[1
]}

Vullo, Alessandro ^{[1
]}

Wilder, Steven P. ^{[1
]}

Zadissa, Amonida ^{[1
]}

Birney, Ewan ^{[1
]}

Harrow, Jennifer ^{[2
]}

Muffato, Matthieu ^{[1
]}

Perry, Emily ^{[1
]}

Ruffier, Magali ^{[1
]}

Spudich, Giulietta ^{[1
]}

Trevanion, Stephen J. ^{[1
]}

Cunningham, Fiona ^{[1
]}

Aken, Bronwen L. ^{[1
]}

Zerbino, Daniel R. ^{[1
]}

Flicek, Paul ^{[1
]}

机构：

[1] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England

[2] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / D1期

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：

ONLINE MENDELIAN INHERITANCE; DATABASE; GENE; EXPRESSION; INTEGRATION; ANNOTATION; EVOLUTION; CATALOG; GENCODE; UPDATE;

D O I：

10.1093/nar/gkv1157

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) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.

引用

页码：D710 / D716

页数：7

共 48 条

[1]

Adzhubei Ivan, 2013, Curr Protoc Hum Genet, VChapter 7, DOI 10.1002/0471142905.hg0720s76

[2] 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

[3] OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders [J].

Amberger, Joanna S. ;

Bocchini, Carol A. ;

Schiettecatte, Francois ;

Scott, Alan F. ;

Hamosh, Ada .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D789-D798

[4]

[Anonymous], ILLUMINA PLATINUM GE

[5] Activities at the Universal Protein Resource (UniProt) [J].

Apweiler, Rolf ;

Bateman, Alex ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Alpi, Emanuele ;

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 ;

Dogan, Tunca ;

Fazzini, Francesco ;

Gane, Paul ;

Castro, Leyla Garcia ;

Garmiri, Penelope ;

Hatton-Ellis, Emma ;

Hieta, Reija ;

Huntley, Rachael ;

Legge, Duncan ;

Liu, Wudong ;

Luo, Jie ;

MacDougall, Alistair ;

Mutowo, Prudence ;

Nightingale, Andrew ;

Orchard, Sandra ;

Pichler, Klemens ;

Poggioli, Diego ;

Pundir, Sangya ;

Pureza, Luis ;

Qi, Guoying ;

Rosanoff, Steven ;

Saidi, Rabie ;

Sawford, Tony ;

Shypitsyna, Aleksandra ;

Turner, Edward ;

Volynkin, Vladimir ;

Wardell, Tony ;

Watkins, Xavier ;

Zellner, Hermann ;

Corbett, Matt .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D191-D198

[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] The variant call format and VCFtools [J].

Danecek, Petr ;

Auton, Adam ;

Abecasis, Goncalo ;

Albers, Cornelis A. ;

Banks, Eric ;

DePristo, Mark A. ;

Handsaker, Robert E. ;

Lunter, Gerton ;

Marth, Gabor T. ;

Sherry, Stephen T. ;

McVean, Gilean ;

Durbin, Richard .

BIOINFORMATICS, 2011, 27 (15) :2156-2158

[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] Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt [J].

Durinck, Steffen ;

Spellman, Paul T. ;

Birney, Ewan ;

Huber, Wolfgang .

NATURE PROTOCOLS, 2009, 4 (08) :1184-1191

[10] COSMIC: exploring the world's knowledge of somatic mutations in human cancer [J].

Forbes, Simon A. ;

Beare, David ;

Gunasekaran, Prasad ;

Leung, Kenric ;

Bindal, Nidhi ;

Boutselakis, Harry ;

Ding, Minjie ;

Bamford, Sally ;

Cole, Charlotte ;

Ward, Sari ;

Kok, Chai Yin ;

Jia, Mingming ;

De, Tisham ;

Teague, Jon W. ;

Stratton, Michael R. ;

McDermott, Ultan ;

Campbell, Peter J. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D805-D811

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