Ensembl 2015

被引：940

作者：

Cunningham, Fiona ^{[1
]}

Amode, M. Ridwan ^{[1
]}

Barrell, Daniel ^{[1
,2
]}

Beal, Kathryn ^{[1
]}

Billis, Konstantinos ^{[1
]}

Brent, Simon ^{[2
]}

Carvalho-Silva, Denise ^{[1
]}

Clapham, Peter ^{[2
]}

Coates, Guy ^{[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
]}

Kaehaeri, Andreas K. ^{[2
]}

Keenan, Stephen ^{[1
]}

Martin, Fergal J. ^{[1
]}

Maurel, Thomas ^{[1
]}

McLaren, William ^{[1
]}

Murphy, Daniel N. ^{[1
,2
]}

Nag, Rishi ^{[1
]}

Overduin, Bert ^{[1
]}

Parker, Anne ^{[1
]}

Patricio, Mateus ^{[1
]}

Perry, Emily ^{[1
]}

Pignatelli, Miguel ^{[1
]}

Riat, Harpreet Singh ^{[1
]}

Sheppard, Daniel ^{[1
]}

Taylor, Kieron ^{[1
]}

Thormann, Anja ^{[1
]}

Vullo, Alessandro ^{[1
]}

Wilder, Steven P. ^{[1
]}

Zadissa, Amonida ^{[1
]}

Aken, Bronwen L. ^{[1
]}

Birney, Ewan ^{[1
]}

Harrow, Jennifer ^{[2
]}

Kinsella, Rhoda ^{[1
]}

Muffato, Matthieu ^{[1
]}

Ruffier, Magali ^{[1
]}

Searle, Stephen M. J. ^{[2
]}

Spudich, Giulietta ^{[1
]}

Trevanion, Stephen J. ^{[1
]}

Yates, Andy ^{[1
]}

Zerbino, Daniel R. ^{[1
]}

Flicek, Paul ^{[1
,2
]}

机构：

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

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

来源：

NUCLEIC ACIDS RESEARCH | 2015年 / 43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：

DATABASE; SEQUENCE; CONSEQUENCES; DISCOVERY; ACCESS; API;

D O I：

10.1093/nar/gku1010

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 (ext-link-type="uri" xlink:href="http://www.ensembl.org" xlink:type="simple">http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (ext-link-type="uri" xlink:href="http://grch37.ensembl.org" xlink:type="simple">http://grch37.ensembl.org). Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (ext-link-type="uri" xlink:href="http://rest.ensembl.org" xlink:type="simple">http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (ext-link-type="uri" xlink:href="https://github.com/Ensembl" xlink:type="simple">https://github.com/Ensembl) under an Apache 2.0 open source license.

引用

页码：D662 / D669

页数：8

共 42 条

[31] Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants [J].

MacArthur, Jacqueline A. L. ;

Morales, Joannella ;

Tully, Ray E. ;

Astashyn, Alex ;

Gil, Laurent ;

Bruford, Elspeth A. ;

Larsson, Pontus ;

Flicek, Paul ;

Dalgleish, Raymond ;

Maglott, Donna R. ;

Cunningham, Fiona .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D873-D878

[32] JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles [J].

Mathelier, Anthony ;

Zhao, Xiaobei ;

Zhang, Allen W. ;

Parcy, Francois ;

Worsley-Hunt, Rebecca ;

Arenillas, David J. ;

Buchman, Sorana ;

Chen, Chih-yu ;

Chou, Alice ;

Ienasescu, Hans ;

Lim, Jonathan ;

Shyr, Casper ;

Tan, Ge ;

Zhou, Michelle ;

Lenhard, Boris ;

Sandelin, Albin ;

Wasserman, Wyeth W. .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D142-D147

[33] UKPMC: a full text article resource for the life sciences [J].

McEntyre, Johanna R. ;

Ananiadou, Sophia ;

Andrews, Stephen ;

Black, William J. ;

Boulderstone, Richard ;

Buttery, Paula ;

Chaplin, David ;

Chevuru, Sandeepreddy ;

Cobley, Norman ;

Coleman, Lee-Ann ;

Davey, Paul ;

Gupta, Bharti ;

Haji-Gholam, Lesley ;

Hawkins, Craig ;

Horne, Alan ;

Hubbard, Simon J. ;

Kim, Jee-Hyub ;

Lewin, Ian ;

Lyte, Vic ;

MacIntyre, Ross ;

Mansoor, Sami ;

Mason, Linda ;

McNaught, John ;

Newbold, Elizabeth ;

Nobata, Chikashi ;

Ong, Ernest ;

Pillai, Sharmila ;

Rebholz-Schuhmann, Dietrich ;

Rosie, Heather ;

Rowbotham, Rob ;

Rupp, C. J. ;

Stoehr, Peter ;

Vaughan, Philip .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D58-D65

[34] Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor [J].

McLaren, William ;

Pritchard, Bethan ;

Rios, Daniel ;

Chen, Yuan ;

Flicek, Paul ;

Cunningham, Fiona .

BIOINFORMATICS, 2010, 26 (16) :2069-2070

[35] Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs [J].

Paten, Benedict ;

Herrero, Javier ;

Beal, Kathryn ;

Fitzgerald, Stephen ;

Birney, Ewan .

GENOME RESEARCH, 2008, 18 (11) :1814-1828

[36] 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

[37] 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

[38] Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models [J].

Shihab, Hashem A. ;

Gough, Julian ;

Cooper, David N. ;

Stenson, Peter D. ;

Barker, Gary L. A. ;

Edwards, Keith J. ;

Day, Ian N. M. ;

Gaunt, Tom R. .

HUMAN MUTATION, 2013, 34 (01) :57-65

[39] TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support [J].

Vergoulis, Thanasis ;

Vlachos, Ioannis S. ;

Alexiou, Panagiotis ;

Georgakilas, George ;

Maragkakis, Manolis ;

Reczko, Martin ;

Gerangelos, Stefanos ;

Koziris, Nectarios ;

Dalamagas, Theodore ;

Hatzigeorgiou, Artemis G. .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D222-D229

[40]

Yates A., 2014, BIOINFORMATICS, V2014

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