UNIT 7.13 Data Storage and Analysis in ArrayExpress and Expression Profiler

  1. Gabriella Rustici,
  2. Misha Kapushesky,
  3. Nikolay Kolesnikov,
  4. Helen Parkinson,
  5. Ugis Sarkans,
  6. Alvis Brazma

Published Online: 1 SEP 2008

DOI: 10.1002/0471250953.bi0713s23

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Rustici, G., Kapushesky, M., Kolesnikov, N., Parkinson, H., Sarkans, U. and Brazma, A. 2008. Data Storage and Analysis in ArrayExpress and Expression Profiler. Current Protocols in Bioinformatics. 23:7.13:7.13.1–7.13.27.

Author Information

  1. European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom

Publication History

  1. Published Online: 1 SEP 2008
  2. Published Print: SEP 2008


ArrayExpress at the European Bioinformatics Institute is a public database for MIAME-compliant microarray and transcriptomics data. It consists of two parts: the ArrayExpress Repository, which is a public archive of microarray data, and the ArrayExpress Warehouse of Gene Expression Profiles, which contains additionally curated subsets of data from the Repository. Archived experiments can be queried by experimental attributes, such as keywords, species, array platform, publication details, or accession numbers. Gene expression profiles can be queried by gene names and properties, such as Gene Ontology terms, allowing expression profiles visualization. The data can be exported and analyzed using the online data analysis tool named Expression Profiler. Data analysis components, such as data preprocessing, filtering, differentially expressed gene finding, clustering methods, and ordination-based techniques, as well as other statistical tools are all available in Expression Profiler, via integration with the statistical package R. Curr. Protoc. Bioinform. 23:7.13.1-7.13.27. © 2008 by John Wiley & Sons, Inc.


  • gene expression;
  • microarrays;
  • transcriptomics;
  • public repository;
  • data analysis