NAR Molecular Biology Database Collection entry number 1294
Petryszak, Robert; Burdett, Tony; Fiorelli, Benedetto; Fonseca, Nuno; Gonzalez-Porta, Mar; Hastings, Emma; Huber, Wolfgang; Jupp, Simon; Keays, Maria; Kryvych, Nataliya; McMurry, Julie; Marioni, John; Malone, James; Megy, Karyn; Rustici, Gabriella; Tang, Amy; Taubert, Jan; Williams, Eleanor; Parkinson, Helen; Brazma, Alvis
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
The Gene Expression Atlas is an added value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments, and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data. A simple interface allows the user to query for differential gene expression either 1) by gene names or attributes such as Gene Ontology terms, or 2) by biological conditions, e.g. diseases, organism parts or cell types. The gene queries return the conditions where expression has been reported, while condition queries return which genes are reported to be expressed in these conditions. A combination of both query types is possible. The query results are ranked using various statistical measures and by how many independent studies in the database show the particular gene-condition association. Currently the database contains information about more than 200,000 genes from 9 species and almost 4,500 biological conditions studied in over 30,000 assays from over 1,000 independent studies.
In addition to the invaluable help from the entire Microarray Team, we would like to thank especially the work of Richard Coulson, Ekaterina Pilicheva, Niran Abeygunawardena and Ugis Sarkans on the gene re-annotation pipeline. Furthermore, the work of Ugis Sarkans, Sergio Contrino and Hugo Berube on the earlier ArrayExpress Warehouse software served as a platform and motivation for the Atlas. We thank also Nikolay Kolesnikov, Andrew Tikhonov, Miroslaw Dylag, and Roby Mani for contributing components and work on maintenance of the infrastructure on which the Atlas service runs. Last but not least, we are grateful to Wolfgang Huber for the invaluable discussions surrounding the Atlas. The project was funded by the EMBL as well as FELICS and EMERALD grants from the European Commission.
Go to the abstract in the NAR 2014 Database Issue.
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