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Nucleic Acids Research Advance Access originally published online on November 10, 2008
Nucleic Acids Research 2009 37(Database issue):D868-D872; doi:10.1093/nar/gkn889
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Nucleic Acids Research, 2009, Vol. 37, Database issue D868-D872
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression

Helen Parkinson1, Misha Kapushesky1, Nikolay Kolesnikov1, Gabriella Rustici1, Mohammad Shojatalab1, Niran Abeygunawardena1, Hugo Berube2, Miroslaw Dylag1, Ibrahim Emam1, Anna Farne1, Ele Holloway1, Margus Lukk1, James Malone1, Roby Mani1, Ekaterina Pilicheva1, Tim F. Rayner3, Faisal Rezwan4, Anjan Sharma1, Eleanor Williams1, Xiangqun Zheng Bradley1, Tomasz Adamusiak1, Marco Brandizi1, Tony Burdett1, Richard Coulson1, Maria Krestyaninova1, Pavel Kurnosov1, Eamonn Maguire1, Sudeshna Guha Neogi1, Philippe Rocca-Serra1, Susanna-Assunta Sansone1, Nataliya Sklyar1, Mengyao Zhao5, Ugis Sarkans1 and Alvis Brazma1,*

1European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK, 2Institute for Information Technology, National Research Council Canada, Ottawa, Ontario, Canada, 3Cambridge Institute for Medical Research, University of Cambridge, Cambridge, 4BioComputation Laboratory, University of Hertfordshire, Hatfield and 5Wellcome Trust Sanger Institute, Hinxton, UK

*To whom correspondence should be addressed. Tel: +44 1223 494658; Fax: +44 1223 494468; Email: brazma{at}ebi.ac.uk

Received September 12, 2008. Revised October 17, 2008. Accepted October 20, 2008.

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.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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