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. 2005 Oct;139(2):632-6.
doi: 10.1104/pp.105.063156.

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress

Gaurab Mukherjee  1 , 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, Mohammadreza Shojatalab
Affiliations

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress

Gaurab Mukherjee et al. Plant Physiol. 2005 Oct.

Abstract

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.

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Figures

Figure 1.
Figure 1.
The sample page of AtMIAMExpress. Note the presence of pull-down lists and controlled vocabularies to reflect consistent annotation.
Figure 2.
Figure 2.
Number of experiments according to organism present in ArrayExpress in May 2005.
See this image and copyright information in PMC

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