Data storage and analysis in ArrayExpress

ArrayExpress is a public resource for microarray data that has two major goals: to serve as an archive providing access to microarray data supporting publications and to build a knowledge base of gene expression profiles. ArrayExpress consists of two tightly integrated databases: ArrayExpress repository, which is an archive, and ArrayExpress data warehouse, which contains reannotated data and is optimized for queries. As of December 2005, ArrayExpress contains gene expression and other microarray data from almost 35,000 hybridizations, comprising over 1200 studies, covering 70 different species. Most data are related to peer-reviewed publications. Password-protected access to prepublication data is provided for reviewers and authors. Data in the repository can be queried by various parameters such as species, authors, or words used in the experiment description. The data warehouse provides a wide range of queries, including ones based on gene and sample properties, and provides capabilities to retrieve data combined from different studies. The ArrayExpress resource also includes Expression Profiler (EP)-a microarray data mining, analysis, and visualization tool-and MIAMExpress-an online data submission tool. This chapter describes all major ArrayExpress components from the user perspective: how to submit to, retrieve from, and analyze data in ArrayExpress.