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Plant Physiology 139:632-636 (2005)
© 2005 American Society of Plant Biologists

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Bioinformatics

Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress

Gaurab Mukherjee*, Niran Abeygunawardena, Helen Parkinson, Sergio Contrino, Steffen Durinck, Anna Farne, Ele Holloway, Per Lilja, Yves Moreau, Ahmet Oezcimen, Tim Rayner, Anjan Sharma, Alvis Brazma, Ugis Sarkans and Mohammadreza Shojatalab

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom (G.M., N.A., H.P., S.C., A.F., E.H., P.L., A.O., T.R., A.S., A.B., U.S., M.S.); and Department of Electronical Engineering, ESAT-SCD, 3001 Leuven-Heverlee, Belgium (S.D., Y.M.)

ArrayExpress is a public microarray repository founded on the Minimum Information About a Microarray Experiment (MIAME) principles that stores MIAME-compliant gene expression data. Plant-based data sets represent approximately one-quarter of the experiments in ArrayExpress. The majority are based on Arabidopsis (Arabidopsis thaliana); however, there are other data sets based on Triticum aestivum, Hordeum vulgare, and Populus subsp. AtMIAMExpress is an open-source Web-based software application for the submission of Arabidopsis-based microarray data to ArrayExpress. AtMIAMExpress exports data in MAGE-ML format for upload to any MAGE-ML-compliant application, such as J-Express and ArrayExpress. It was designed as a tool for users with minimal bioinformatics expertise, has comprehensive help and user support, and represents a simple solution to meeting the MIAME guidelines for the Arabidopsis community. Plant data are queryable both in ArrayExpress and in the Data Warehouse databases, which support queries based on gene-centric and sample-centric annotation. The AtMIAMExpress submission tool is available at http://www.ebi.ac.uk/at-miamexpress/. The software is open source and is available from http://sourceforge.net/projects/miamexpress/. For information, contact miamexpress@ebi.ac.uk.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.063156.

* Corresponding author; e-mail gaurab{at}ebi.ac.uk; fax 44–(0)–1223–494468.

Received March 21, 2005; returned for revision June 10, 2005; accepted June 24, 2005.




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