ArrayExpress update - From an archive of functional genomics experiments to the atlas of gene expression

H. Parkinson; M. Kapushesky; N. Kolesnikov; G. Rustici; M. Shojatalab; N. Abeygunawardena; H. Berube; M. Dylag; I. Emam; A. Farne; E. Holloway; M. Lukk; J. Malone; R. Mani; E. Pilicheva; T.F. Rayner; F. Rezwan; A. Sharma; E. Williams; X.Z. Bradley; T. Adamusiak; M. Brandizi; T. Burdett; R. Coulson; M. Krestyaninova; P. Kurnosov; E. Maguire; S.G. Neogi; P. Rocca-Serra; S.-A. Sansone; N. Sklyar; M. Zhao; U. Sarkans; A. Brazma

doi:10.1093/nar/gkn889

ArrayExpress update - From an archive of functional genomics experiments to the atlas of gene expression

H. Parkinson, M. Kapushesky, N. Kolesnikov, G. Rustici, M. Shojatalab, N. Abeygunawardena, H. Berube, M. Dylag, I. Emam, A. Farne, E. Holloway, M. Lukk, J. Malone, R. Mani, E. Pilicheva, T.F. Rayner, F. Rezwan, A. Sharma, E. Williams, X.Z. BradleyT. Adamusiak, M. Brandizi, T. Burdett, R. Coulson, M. Krestyaninova, P. Kurnosov, E. Maguire, S.G. Neogi, P. Rocca-Serra, S.-A. Sansone, N. Sklyar, M. Zhao, U. Sarkans, A. Brazma

Research output: Contribution to journal › Article › peer-review

353 Citations (Scopus)

Abstract

ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse—a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas—a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200 000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently—ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.

Original language	English
Pages (from-to)	D868-D872
Number of pages	5
Journal	Nucleic Acids Research
Volume	37
Issue number	suppl_1
Early online date	10 Nov 2008
DOIs	https://doi.org/10.1093/nar/gkn889
Publication status	Published - 01 Jan 2009
Externally published	Yes

Keywords

Databases, Genetic
Gene Expression Profiling
Genomics
Oligonucleotide Array Sequence Analysis

Access to Document

10.1093/nar/gkn889Licence: CC BY-NC

Permanent link

Persistent link

Cite this

Parkinson, H., Kapushesky, M., Kolesnikov, N., Rustici, G., Shojatalab, M., Abeygunawardena, N., Berube, H., Dylag, M., Emam, I., Farne, A., Holloway, E., Lukk, M., Malone, J., Mani, R., Pilicheva, E., Rayner, T. F., Rezwan, F., Sharma, A., Williams, E., ... Brazma, A. (2009). ArrayExpress update - From an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Research, 37(suppl_1), D868-D872. https://doi.org/10.1093/nar/gkn889

@article{76ef4b1739e043279ca111a0f09c1710,

title = "ArrayExpress update - From an archive of functional genomics experiments to the atlas of gene expression",

abstract = "ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse—a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas—a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200 000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently—ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.",

keywords = "Databases, Genetic, Gene Expression Profiling, Genomics, Oligonucleotide Array Sequence Analysis",

author = "H. Parkinson and M. Kapushesky and N. Kolesnikov and G. Rustici and M. Shojatalab and N. Abeygunawardena and H. Berube and M. Dylag and I. Emam and A. Farne and E. Holloway and M. Lukk and J. Malone and R. Mani and E. Pilicheva and T.F. Rayner and F. Rezwan and A. Sharma and E. Williams and X.Z. Bradley and T. Adamusiak and M. Brandizi and T. Burdett and R. Coulson and M. Krestyaninova and P. Kurnosov and E. Maguire and S.G. Neogi and P. Rocca-Serra and S.-A. Sansone and N. Sklyar and M. Zhao and U. Sarkans and A. Brazma",

note = "Funding Information: The European Molecular Biology Laboratory; the European Commission grants FELICS (021902); EMERALD (LSHG-CT-2006-037689); DIAMONDS (LSHG-CT-2004-512143); BioSapiens (LSHG-CT-2003-503265); MolPAGE (LSHG-CT-2004-512066); MUGEN (LSHG-CT-2005-005203); Carcinogenomics (LSHB-2006-037712); Nutrigenomics (NoE-503630); Biotechnology and Biological Sciences Research Council (BB/E025080/ 1); the MAGE grant from National Human Genome Research Institute and National Institute of Biomedical Imaging and Bioengineering from the National Institute of Health (1 P41 HG003619-01). Funding for open access charge: European Molecular Biology Laboratory.",

year = "2009",

month = jan,

day = "1",

doi = "10.1093/nar/gkn889",

language = "English",

volume = "37",

pages = "D868--D872",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "suppl_1",

}

Parkinson, H, Kapushesky, M, Kolesnikov, N, Rustici, G, Shojatalab, M, Abeygunawardena, N, Berube, H, Dylag, M, Emam, I, Farne, A, Holloway, E, Lukk, M, Malone, J, Mani, R, Pilicheva, E, Rayner, TF, Rezwan, F, Sharma, A, Williams, E, Bradley, XZ, Adamusiak, T, Brandizi, M, Burdett, T, Coulson, R, Krestyaninova, M, Kurnosov, P, Maguire, E, Neogi, SG, Rocca-Serra, P, Sansone, S-A, Sklyar, N, Zhao, M, Sarkans, U & Brazma, A 2009, 'ArrayExpress update - From an archive of functional genomics experiments to the atlas of gene expression', Nucleic Acids Research, vol. 37, no. suppl_1, pp. D868-D872. https://doi.org/10.1093/nar/gkn889

TY - JOUR

T1 - ArrayExpress update - From an archive of functional genomics experiments to the atlas of gene expression

AU - Parkinson, H.

AU - Kapushesky, M.

AU - Kolesnikov, N.

AU - Rustici, G.

AU - Shojatalab, M.

AU - Abeygunawardena, N.

AU - Berube, H.

AU - Dylag, M.

AU - Emam, I.

AU - Farne, A.

AU - Holloway, E.

AU - Lukk, M.

AU - Malone, J.

AU - Mani, R.

AU - Pilicheva, E.

AU - Rayner, T.F.

AU - Rezwan, F.

AU - Sharma, A.

AU - Williams, E.

AU - Bradley, X.Z.

AU - Adamusiak, T.

AU - Brandizi, M.

AU - Burdett, T.

AU - Coulson, R.

AU - Krestyaninova, M.

AU - Kurnosov, P.

AU - Maguire, E.

AU - Neogi, S.G.

AU - Rocca-Serra, P.

AU - Sansone, S.-A.

AU - Sklyar, N.

AU - Zhao, M.

AU - Sarkans, U.

AU - Brazma, A.

N1 - Funding Information: The European Molecular Biology Laboratory; the European Commission grants FELICS (021902); EMERALD (LSHG-CT-2006-037689); DIAMONDS (LSHG-CT-2004-512143); BioSapiens (LSHG-CT-2003-503265); MolPAGE (LSHG-CT-2004-512066); MUGEN (LSHG-CT-2005-005203); Carcinogenomics (LSHB-2006-037712); Nutrigenomics (NoE-503630); Biotechnology and Biological Sciences Research Council (BB/E025080/ 1); the MAGE grant from National Human Genome Research Institute and National Institute of Biomedical Imaging and Bioengineering from the National Institute of Health (1 P41 HG003619-01). Funding for open access charge: European Molecular Biology Laboratory.

PY - 2009/1/1

Y1 - 2009/1/1

N2 - ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse—a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas—a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200 000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently—ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.

AB - ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse—a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas—a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200 000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently—ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.

KW - Databases, Genetic

KW - Gene Expression Profiling

KW - Genomics

KW - Oligonucleotide Array Sequence Analysis

UR - http://www.scopus.com/inward/record.url?scp=58149204055&partnerID=8YFLogxK

U2 - 10.1093/nar/gkn889

DO - 10.1093/nar/gkn889

M3 - Article

C2 - 19015125

SN - 0305-1048

VL - 37

SP - D868-D872

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - suppl_1

ER -

ArrayExpress update - From an archive of functional genomics experiments to the atlas of gene expression

Abstract

Keywords

Access to Document

Permanent link

Other files and links

Fingerprint

Cite this