T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research

被引：58

作者：

Burren, Oliver S. ^{[1
]}

Adlem, Ellen C. ^{[1
]}

Achuthan, Premanand ^{[1
]}

Christensen, Mikkel ^{[1
]}

Coulson, Richard M. R. ^{[1
]}

Todd, John A. ^{[1
]}

机构：

[1] Univ Cambridge, Cambridge Inst Med Res, Juvenile Diabet Res Fdn, Wellcome Trust Diabet & Inflammat Lab, Cambridge CB2 0XY, England

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

基金：

英国惠康基金;

关键词：

GENOME-WIDE ASSOCIATION; EXPRESSION; MODEL; METAANALYSIS; BROWSER; BIOLOGY; RISK; LOCI; RAT;

D O I：

10.1093/nar/gkq912

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：

T1DBase (http://www.t1dbase.org) is web platform, which supports the type 1 diabetes (T1D) community. It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. This update describes the incorporation of new data sets, tools and curation efforts as well as a new website design to simplify site use. New data sets include curated summary data from four genome-wide association studies relevant to T1D, HaemAtlas-a data set and tool to query gene expression levels in haematopoietic cells and a manually curated table of human T1D susceptibility loci, incorporating genetic overlap with other related diseases. These developments will continue to support T1D research and allow easy access to large and complex T1D relevant data sets.

引用

页码：D997 / D1001

页数：5

共 34 条

[1]

[Anonymous], 2005, R LANG ENV STAT COMP

[2] Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes [J].

Barrett, Jeffrey C. ;

Clayton, David G. ;

Concannon, Patrick ;

Akolkar, Beena ;

Cooper, Jason D. ;

Erlich, Henry A. ;

Julier, Cecile ;

Morahan, Grant ;

Nerup, Jorn ;

Nierras, Concepcion ;

Plagnol, Vincent ;

Pociot, Flemming ;

Schuilenburg, Helen ;

Smyth, Deborah J. ;

Stevens, Helen ;

Todd, John A. ;

Walker, Neil M. ;

Rich, Stephen S. .

NATURE GENETICS, 2009, 41 (06) :703-707

[3] The Mouse Genome Database (MGD): mouse biology and model systems [J].

Bult, Carol J. ;

Eppig, Janan T. ;

Kadin, James A. ;

Richardson, Joel E. ;

Blake, Judith A. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D724-D728

[4] Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls [J].

Burton, Paul R. ;

Clayton, David G. ;

Cardon, Lon R. ;

Craddock, Nick ;

Deloukas, Panos ;

Duncanson, Audrey ;

Kwiatkowski, Dominic P. ;

McCarthy, Mark I. ;

Ouwehand, Willem H. ;

Samani, Nilesh J. ;

Todd, John A. ;

Donnelly, Peter ;

Barrett, Jeffrey C. ;

Davison, Dan ;

Easton, Doug ;

Evans, David ;

Leung, Hin-Tak ;

Marchini, Jonathan L. ;

Morris, Andrew P. ;

Spencer, Chris C. A. ;

Tobin, Martin D. ;

Attwood, Antony P. ;

Boorman, James P. ;

Cant, Barbara ;

Everson, Ursula ;

Hussey, Judith M. ;

Jolley, Jennifer D. ;

Knight, Alexandra S. ;

Koch, Kerstin ;

Meech, Elizabeth ;

Nutland, Sarah ;

Prowse, Christopher V. ;

Stevens, Helen E. ;

Taylor, Niall C. ;

Walters, Graham R. ;

Walker, Neil M. ;

Watkins, Nicholas A. ;

Winzer, Thilo ;

Jones, Richard W. ;

McArdle, Wendy L. ;

Ring, Susan M. ;

Strachan, David P. ;

Pembrey, Marcus ;

Breen, Gerome ;

St Clair, David ;

Caesar, Sian ;

Gordon-Smith, Katherine ;

Jones, Lisa ;

Fraser, Christine ;

Green, Elain K. .

NATURE, 2007, 447 (7145) :661-678

[5] OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups [J].

Chen, Feng ;

Mackey, Aaron J. ;

Stoeckert, Christian J., Jr. ;

Roos, David S. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D363-D368

[6] An R package for analysis of whole-genome association studies [J].

Clayton, David ;

Leung, Hin-Tak .

HUMAN HEREDITY, 2007, 64 (01) :45-51

[7] Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci [J].

Cooper, Jason D. ;

Smyth, Deborah J. ;

Smiles, Adam M. ;

Plagnol, Vincent ;

Walker, Neil M. ;

Allen, James E. ;

Downes, Kate ;

Barrett, Jeffrey C. ;

Healy, Barry C. ;

Mychaleckyj, Josyf C. ;

Warram, James H. ;

Todd, John A. .

NATURE GENETICS, 2008, 40 (12) :1399-1401

[8] Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data [J].

Degner, Jacob F. ;

Marioni, John C. ;

Pai, Athma A. ;

Pickrell, Joseph K. ;

Nkadori, Everlyne ;

Gilad, Yoav ;

Pritchard, Jonathan K. .

BIOINFORMATICS, 2009, 25 (24) :3207-3212

[9] The Distributed Annotation System [J].

Dowell, Robin D. ;

Jokerst, Rodney M. ;

Day, Allen ;

Eddy, Sean R. ;

Stein, Lincoln .

BMC BIOINFORMATICS, 2001, 2 (1)

[10] A second generation human haplotype map of over 3.1 million SNPs [J].

Frazer, Kelly A. ;

Ballinger, Dennis G. ;

Cox, David R. ;

Hinds, David A. ;

Stuve, Laura L. ;

Gibbs, Richard A. ;

Belmont, John W. ;

Boudreau, Andrew ;

Hardenbol, Paul ;

Leal, Suzanne M. ;

Pasternak, Shiran ;

Wheeler, David A. ;

Willis, Thomas D. ;

Yu, Fuli ;

Yang, Huanming ;

Zeng, Changqing ;

Gao, Yang ;

Hu, Haoran ;

Hu, Weitao ;

Li, Chaohua ;

Lin, Wei ;

Liu, Siqi ;

Pan, Hao ;

Tang, Xiaoli ;

Wang, Jian ;

Wang, Wei ;

Yu, Jun ;

Zhang, Bo ;

Zhang, Qingrun ;

Zhao, Hongbin ;

Zhao, Hui ;

Zhou, Jun ;

Gabriel, Stacey B. ;

Barry, Rachel ;

Blumenstiel, Brendan ;

Camargo, Amy ;

Defelice, Matthew ;

Faggart, Maura ;

Goyette, Mary ;

Gupta, Supriya ;

Moore, Jamie ;

Nguyen, Huy ;

Onofrio, Robert C. ;

Parkin, Melissa ;

Roy, Jessica ;

Stahl, Erich ;

Winchester, Ellen ;

Ziaugra, Liuda ;

Altshuler, David ;

Shen, Yan .

NATURE, 2007, 449 (7164) :851-U3

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