Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.
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.
Mukherjee
Gaurab
G
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. gaurab@ebi.ac.uk
Abeygunawardena
Niran
N
Parkinson
Helen
H
Contrino
Sergio
S
Durinck
Steffen
S
Farne
Anna
A
Holloway
Ele
E
Lilja
Per
P
Moreau
Yves
Y
Oezcimen
Ahmet
A
Rayner
Tim
T
Sharma
Anjan
A
Brazma
Alvis
A
Sarkans
Ugis
U
Shojatalab
Mohammadreza
M
D000047:Academies and Institutes; D017360:Arabidopsis / Q000235:genetics*; D019295:Computational Biology; D030541:Databases, Genetic; D005060:Europe; D020869:Gene Expression Profiling; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D014908:Triticum / Q000235:genetics