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An enhanced tool for storage and mining of genome-wide expression data

 
  December, 4 2008 20:28
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Functional genomics is expected to revolutionize biological and biomedical research. In this context, public repositories of microarray data are key elements that allow the open interchange and analysis of results from genome-wide expression experiments.

An in press paper in Nucleic Acid Research describes the latest version of one of those public repositories: ArrayExpress. ArrayExpress is a web server from the European Bioinformatics Institute (EBI) that allows access to a large repository of microarray data (over 6000 studies, representing around 200.000 hybridizations and hundreds of millions of individual gene expression measurements). It has three main components: the Repository (raw data and associated info for all the available datasets), the Warehouse (including gene expression profiles for a subset of experiments) and the Atlas (which gives access to summaries of expression data across different experiments). ArrayExpress also includes data from high-throughput genotyping and sequencing experiments.

There are some recent developments: the latest version of ArrayExpress also imports datasets from NCBI GEO (one of the other main public repositories) and it is possible to import automatically datasets from ArrayExpress to Bioconductor (one of the most complete set of tools for genomics analysis) and to ExpressionProfiler (an expression data analysis tool available at the EBI website).

It is expected that the current efforts to facilitate submission of data will lead to an even higher inclusion of datasets reported in scientific papers and that this enhanced online tool will continue to be helpful for the researchers working in both the experimental and in silico aspects of functional genomics.

Author: Alvis Brazma, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK. E-mail: brazma@ebi.ac.uk

Reference:

Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res. 2008, in press.

Paper available online.

The ArrayExpress server is available at the ArrayExpress website


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