title: ArrayExpress update--simplifying data submissions.
abstract: The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is an international functional genomics database at the European Bioinformatics Institute (EMBL-EBI) recommended by most journals as a repository for data supporting peer-reviewed publications. It contains data from over 7000 public sequencing and 42,000 array-based studies comprising over 1.5 million assays in total. The proportion of sequencing-based submissions has grown significantly over the last few years and has doubled in the last 18 months, whilst the rate of microarray submissions is growing slightly. All data in ArrayExpress are available in the MAGE-TAB format, which allows robust linking to data analysis and visualization tools and standardized analysis. The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold. In the near future, Annotare will become the only submission route into ArrayExpress, alongside MAGE-TAB format-based pipelines. ArrayExpress is a stable and highly accessed resource. Our future tasks include automation of data flows and further integration with other EMBL-EBI resources for the representation of multi-omics data.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Kolesnikov
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Emma
authors.initials: E
authors.lastname: Hastings
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Maria
authors.initials: M
authors.lastname: Keays
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Olga
authors.initials: O
authors.lastname: Melnichuk
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Y Amy
authors.initials: YA
authors.lastname: Tang
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Eleanor
authors.initials: E
authors.lastname: Williams
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Miroslaw
authors.initials: M
authors.lastname: Dylag
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Natalja
authors.initials: N
authors.lastname: Kurbatova
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Marco
authors.initials: M
authors.lastname: Brandizi
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Tony
authors.initials: T
authors.lastname: Burdett
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Karyn
authors.initials: K
authors.lastname: Megy
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Pilicheva
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK School of Biological Sciences, Cambridge Systems Biology Centre, Tennis Court Road, Cambridge, CB2 1QR, UK.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rustici
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Tikhonov
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Helen
authors.initials: H
authors.lastname: Parkinson
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Robert
authors.initials: R
authors.lastname: Petryszak
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.
authors.forename: Ugis
authors.initials: U
authors.lastname: Sarkans
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK brazma@ebi.ac.uk.
authors.forename: Alvis
authors.initials: A
authors.lastname: Brazma
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software