Features of the AE object model MIAME-compliant able to import MAML-formatted data supports raw and processed data independence of: experimental platforms image analysis methods data normalization methods object model-based query mechanism
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ArrayExpress – a public repository for microarray data
Alvis Brazma, Ugis Sarkans, Helen Parkinson, Alan Robinson, Mohammadreza Shojatalab, Jaak ViloEBI, European Molecular Biology Laboratory Outstation – Hinxton (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
The European Bioinformatics Institute is establishing a public repository for microarray based gene expression data ArrayExpress
Alvis Brazma, Johan Rung, Ugis Sarkans, Thomas Schlitt, Jaak ViloEuropean Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Microarrays, one of the latest breakthroughs in experimental molecular biology, are producing considerable amounts of gene expression and other functional genomics data. The handling, storage, and analysis of these data are becoming the major bottlenecks in the utilization of the microarray technology. Storing and annotating these data is not a trivial problem due to many reasons. The raw microarray data are images, which have to be transformed into gene expression matrices -- tables, where rows represent genes, columns represent various samples such as different tissues, and values at each position characterizing the expression level of the particular gene in the particular sample. This process is not a trivial one due to replicate measurements, replicate spots, different oligos reporting information about the expression level of the same gene, problems with sequence homology and potential cross-hybridisation, cross-platform comparisons, and so forth.
The high-level gene expression matrices representing genes and respective expression levels, also have to be integrated with other genomic data and analysed further, if any knowledge about the underlying biological processes is to be extracted (see ). The European Bioinformatics Institute initiated an international effort to establish standards for microarray data representation, annotation and exchange . Recommendations of MIAME - The Minimum Information About a Microarray Experiment - specify the minimum information that must be reported about a microarray (or any DNA array) based gene expression monitoring experiment in order to ensure the interpretability, as well as potential verification of the results by third parties. An XML based data exchange format - Microarray Markup Language (MAML) is being developed in collaboration with Microarray Gene Expression Database (MGED) Group (see www.mged.org).
EBI is establishing a database ArrayExpress, a public repository for microarray data, which will accept data in MAML format. Expression Profiler, a set of online tools for gene expression data analysis has been developed at the EBI and is available for public use (www.ebi.ac.uk/microarray).
The analysis software in the Expression Profiler facilitates the clustering, exploration, and visualization of the gene expression data, as well as linking the analysis results to tools and databases elsewhere. Expression Profiler includes tools that assist with the analysis of expression data in connection with other data types. Currently, the DNA sequence data can be analysed and visualized as well as expression data, permitting users to discover, study, and visualize putative transcription factor binding sites .
One of the prospects of analysing microarray data is a reverse engineering of gene regulatory networks from gene expression and other genomics data. We have been successfully using our tools for in silico prediction of transcription factor binding sites . Furthermore, we are developing models for describing gene regulatory networks, and use this modelling approach to find insights into the regulation of gene expression in response to the activity of other molecules in the cell as well as extracellular signals.
EBI is organising an EMBO course:
Analysis and Informatics of DNA-Array Gene Expression data
(October 29 – November 3)
For more information and applications see www.ebi.ac.uk/microarray/
Prototype of AE query interface
A web based tool for microarray data analysis (see poster by J. Vilo)
ArrayExpress model - conceptual design
A simplified version of AE object model