title: Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.
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.
authors.affiliation: EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. gaurab@ebi.ac.uk
authors.forename: Gaurab
authors.initials: G
authors.lastname: Mukherjee
authors.forename: Niran
authors.initials: N
authors.lastname: Abeygunawardena
authors.forename: Helen
authors.initials: H
authors.lastname: Parkinson
authors.forename: Sergio
authors.initials: S
authors.lastname: Contrino
authors.forename: Steffen
authors.initials: S
authors.lastname: Durinck
authors.forename: Anna
authors.initials: A
authors.lastname: Farne
authors.forename: Ele
authors.initials: E
authors.lastname: Holloway
authors.forename: Per
authors.initials: P
authors.lastname: Lilja
authors.forename: Yves
authors.initials: Y
authors.lastname: Moreau
authors.forename: Ahmet
authors.initials: A
authors.lastname: Oezcimen
authors.forename: Tim
authors.initials: T
authors.lastname: Rayner
authors.forename: Anjan
authors.initials: A
authors.lastname: Sharma
authors.forename: Alvis
authors.initials: A
authors.lastname: Brazma
authors.forename: Ugis
authors.initials: U
authors.lastname: Sarkans
authors.forename: Mohammadreza
authors.initials: M
authors.lastname: Shojatalab
mesh_terms: 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