NCBI GEO: archive for functional genomics data sets-update

被引:6871
作者
Barrett, Tanya [1 ]
Wilhite, Stephen E. [1 ]
Ledoux, Pierre [1 ]
Evangelista, Carlos [1 ]
Kim, Irene F. [1 ]
Tomashevsky, Maxim [1 ]
Marshall, Kimberly A. [1 ]
Phillippy, Katherine H. [1 ]
Sherman, Patti M. [1 ]
Holko, Michelle [1 ]
Yefanov, Andrey [1 ]
Lee, Hyeseung [1 ]
Zhang, Naigong [1 ]
Robertson, Cynthia L. [1 ]
Serova, Nadezhda [1 ]
Davis, Sean [2 ]
Soboleva, Alexandra [1 ]
机构
[1] NCI, Natl Ctr Biotechnol Informat, Natl Lib Med, NIH, Bethesda, MD 20892 USA
[2] NCI, Mol Genet Sect, Genet Branch, NIH, Bethesda, MD 20892 USA
基金
美国国家卫生研究院;
关键词
GENE-EXPRESSION;
D O I
10.1093/nar/gks1193
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 Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.
引用
收藏
页码:D991 / D995
页数:5
相关论文
共 19 条
  • [2] Gene data to hit milestone
    Baker, Monya
    [J]. NATURE, 2012, 487 (7407) : 282 - 283
  • [3] BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
    Barrett, Tanya
    Clark, Karen
    Gevorgyan, Robert
    Gorelenkov, Vyacheslav
    Gribov, Eugene
    Karsch-Mizrachi, Ilene
    Kimelman, Michael
    Pruitt, Kim D.
    Resenchuk, Sergei
    Tatusova, Tatiana
    Yaschenko, Eugene
    Ostell, James
    [J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) : D57 - D63
  • [4] NCBI GEO: archive for functional genomics data sets-10 years on
    Barrett, Tanya
    Troup, Dennis B.
    Wilhite, Stephen E.
    Ledoux, Pierre
    Evangelista, Carlos
    Kim, Irene F.
    Tomashevsky, Maxim
    Marshall, Kimberly A.
    Phillippy, Katherine H.
    Sherman, Patti M.
    Muertter, Rolf N.
    Holko, Michelle
    Ayanbule, Oluwabukunmi
    Yefanov, Andrey
    Soboleva, Alexandra
    [J]. NUCLEIC ACIDS RESEARCH, 2011, 39 : D1005 - D1010
  • [5] NCBI GEO: archive for high-throughput functional genomic data
    Barrett, Tanya
    Troup, Dennis B.
    Wilhite, Stephen E.
    Ledoux, Pierre
    Rudnev, Dmitry
    Evangelista, Carlos
    Kim, Irene F.
    Soboleva, Alexandra
    Tomashevsky, Maxim
    Marshall, Kimberly A.
    Phillippy, Katherine H.
    Sherman, Patti M.
    Muertter, Rolf N.
    Edgar, Ron
    [J]. NUCLEIC ACIDS RESEARCH, 2009, 37 : D885 - D890
  • [6] 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
  • [7] Minimum information about a microarray experiment (MIAME) - toward standards for microarray data
    Brazma, A
    Hingamp, P
    Quackenbush, J
    Sherlock, G
    Spellman, P
    Stoeckert, C
    Aach, J
    Ansorge, W
    Ball, CA
    Causton, HC
    Gaasterland, T
    Glenisson, P
    Holstege, FCP
    Kim, IF
    Markowitz, V
    Matese, JC
    Parkinson, H
    Robinson, A
    Sarkans, U
    Schulze-Kremer, S
    Stewart, J
    Taylor, R
    Vilo, J
    Vingron, M
    [J]. NATURE GENETICS, 2001, 29 (04) : 365 - 371
  • [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] Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    Edgar, R
    Domrachev, M
    Lash, AE
    [J]. NUCLEIC ACIDS RESEARCH, 2002, 30 (01) : 207 - 210
  • [10] NCBI Epigenomics: a new public resource for exploring epigenomic data sets
    Fingerman, Ian M.
    McDaniel, Lee
    Zhang, Xuan
    Ratzat, Walter
    Hassan, Tarek
    Jiang, Zhifang
    Cohen, Robert F.
    Schuler, Gregory D.
    [J]. NUCLEIC ACIDS RESEARCH, 2011, 39 : D908 - D912