Gene Expression Atlas
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* What is ArrayExpress Gene Expression Atlas The ArrayExpress Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. To cite the Atlas in your research or to learn more about it, please refer to Kapushesky M et al. (2010), "Gene Expression Atlas at the European Bioinformatics Institute", Nucleic Acids Research Database Issue 2010, http://nar.oxfordjournals.org/cgi/content/full/gkp936?ijkey=zMCQ9oPVLrhe7zk&keytype=ref. The EBI Gene Expression Atlas is running at http://www-test.ebi.ac.uk/gxa. * Features of ArrayExpress Gene Expression Atlas + Standalone: only an Oracle RDBMS, R/Bioconductor and a Java Web App server required + Import your MAGE-TAB (http://www.mged.org/mage-tab) formatted data directly + Public curated EBI Gene Expression Atlas available in monthly releases on FTP + Statistical meta-analysis using R/Bioconductor + Semantic enrichment with the Experimental Factor Ontology (EFO, http://www.ebi.ac.uk/efo) + Powerful search and visualization interface The ArrayExpress Gene Expression Atlas project is hosted at the EBI at: * Getting Gene Expression Atlas You can get the source code and read the installation instructions at our GitHub Repository at: http://github.com/gxa/gxa. The EBI data dumps are available at ftp://aexpress:firstname.lastname@example.org/atlas2. You can subscribe to our mailing list and email your questions, feedback and suggestions at: email@example.com for further information. * How to install You will need an Oracle database, an R/Bioconductor installation and a web server that can run Java Web Applications, e.g., Apache Tomcat. For more detail, read the instructions at: http://wiki.github.com/gxa/gxa/installation * Authors Project Leader: Misha Kapushesky (firstname.lastname@example.org) Development Team: Robert Petryszak, Olga Melnichuk, Nataliya Sklyar Former Developers: Tony Burdett, Pavel Kurnosov, Andrey Zorin, Nikolay Pultsin, Alexey Filippov * License and Copyright Licensed under the Apache License, Version 2.0. Copyright 2008-2012 Microarray Informatics Team, EMBL-European Bioinformatics Institute.