The ArrayExpress repository is a MIAME compliant (2
) primary archive containing the original data related to publications or generated by consortia. ArrayExpress is one of the three databases recommended by the MGED society (3
) for depositions of publication related microarray data the other two being Gene Expression Omnibus (4
) and CiBEX (5
). ArrayExpress provides the means to store pre-publication data confidentially whilst allowing access to authorized users such as journal editors and referees. The data are made publicly available upon publication of the paper to which they relate. During the last 2 years the ArrayExpress Repository has grown 5-fold to over 50
000 hybridizations (September 2006) organized into 1650 different experiments. More than 90% of the experiments relate to gene expression profiling studies, the remainder are array based chromatin immunoprecipitation or comparative genomics experiments. Over 200 different organisms are represented, the largest contributors being human, mouse, Arabidopsis, yeast and rat.
A new ArrayExpress experiment browse and query interface ( and ) was released in 2006. It allows the user to browse the entire content of the database in a summary view or query public datasets using free text and displays the query results in a summary view of up to 500 experiments per page which can be sorted by name, accession number and load date, and filtered by array design, species, date or availability of raw and processed data. For example, the user can query for all experiments containing the phrase ‘bone marrow’ in their description, or retrieve experiments by accession numbers (e.g. E-TABM-102), publication details, array design names and journal names.
ArrayExpress experiment query form. Queries on experiment properties: organisms, author's names, array types or accession numbers are supported.
A detailed view of an experiment from the repository. Strings matching the query terms are highlighted in yellow.
Each row in the summary view can be expanded to a detailed view including experiment description and publication references. Queries can also be exported to spreadsheets and saved. There are links to the original data files where filled or empty icons indicate the presence or absence of raw or normalized data. Each experiment has a link to spreadsheets and graphs describing the sample properties and experiment design. Linking to the ‘Detailed data retrieval page’ allows for selection of particular Quantitation Types (e.g. signal or log ratio) from multiple data files for specific conditions. These can be exported into a single data matrix for download, or uploaded to Expression profiler, an online data analysis tool for further processing. An advanced query interface is also provided http://www.ebi.ac.uk/aerep
for password-protected access to private data and complex queries, e.g. all experiments performed on a specific array and complex combinations of species/experiments.