ArrayExpress update—trends in database growth and links to data analysis tools

Gabriella Rustici(European Bioinformatics Institute), N. N. Kolesnikov(Wellcome Sanger Institute), Marco Brandizi(European Bioinformatics Institute), Tony Burdett(European Bioinformatics Institute), Miroslaw Dylag(Wellcome Sanger Institute), Ibrahim Emam(Wellcome Sanger Institute), Anna Farne(Wellcome Sanger Institute), Emma Hastings(European Bioinformatics Institute), Jon Ison(European Bioinformatics Institute), Maria Keays(Wellcome Sanger Institute), Natalja Kurbatova(Wellcome Sanger Institute), James Malone(Wellcome Sanger Institute), Roby Mani(European Bioinformatics Institute), Annalisa Mupo(European Bioinformatics Institute), Rui Pedro Pereira(European Bioinformatics Institute), Ekaterina Pilicheva(Wellcome Sanger Institute), Johan Rung(Wellcome Sanger Institute), Anjan Sharma(European Bioinformatics Institute), Amy Tang(European Bioinformatics Institute), Tobias Ternent(Wellcome Sanger Institute), Andrew Tikhonov(Wellcome Sanger Institute), Danielle Welter(Wellcome Sanger Institute), Eleanor Williams(Wellcome Sanger Institute), Alvis Brāzma(Wellcome Sanger Institute), Helen Parkinson(European Bioinformatics Institute), Uğis Sarkans(Wellcome Sanger Institute)
Nucleic Acids Research
November 26, 2012
10.1093/nar/gks1174
Cited by 375Open Access
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Abstract

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.

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