QLK3-2002-02035 Compendium of Arabidopsis gene expression (CAGE)

Contacts
Website: jic-bioinfo.bbsrc.ac.uk/CATMA/).




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Type of Project	Demonstration
Contract No	QLK3-2002-02035
Total Cost
EC Contribution	3,348,900 EUR
Start Date	01-11-2002
Duration	36 Months

Abstract

The CAGE project will demonstrate the power of a concerted effort to build a gene expression knowledge base. A consortium of European Arabidopsis functional genomics centres has teamed up with bioinformatics partners that contribute expertise in microarray data processing, analysis and storage/distribution. A total of 2 000 Arabidopsis samples will be produced and analysed under largely standardised conditions. These samples will be profiled on CATMA microarrays containing gene-specific probes for most Arabidopsis genes, to build a prototype compendium of expression profiles. The data will be assessed for statistical significance and submitted to the ArrayExpress database at the European Bioinformatics Institute (EBI). EBI will deliver specific CAGE ontology, and data submission pipelines. The compendium data will be annotated and analysed for content and confirmation of gene function. The compendium will be maintained by EBI.

Objectives

The objectives are to:

• demonstrate the utility of the CATMA array (a novel microarray format for whole-genome Arabidopsis transcription profiling
• deliver a prototype compendium of Arabidopsis expression profiles which is a catalogue of molecular phenotypes describing plant development and function; such a catalogue will be a reference for future transcription analysis in Arabidopsis as it will be maintained and accessible through the European Bioinformatics Institute.
• demonstrate that adherence to guidelines, standard protocols and procedures will generate added value through coherence and quality of data.
• establish data submission and processing pipelines, and analytical tools for the European research community, facilitating future genome-wide Arabidopsis transcription profiling.

Activities

Arabidopsis functional genomics today faces the immense challenge to map genomic sequence to function since most of the 25 000 or more genes identified in the Arabidopsis genome have not been characterised experimentally. A particularly powerful technology for the association of gene-to-function is microarray-based expression analysis. In the CAGE project we will build a publicly available functional genomics knowledge base using the novel CATMA microarray. The project will demonstrate both the power of this microarray (designed to discriminate highly between gene homologues), and the added value of analysis of microarray data in a compendium format.

To successfully accomplish this we have brought together a consortium of European laboratories including a series of plant research centres and partners that excel in developing statistics and mining algorithms for the analysis of gene expression. All microarrays will be produced by VIB-MAF, thereby controlling variance and reducing cost.

A total of 4 000 microarrays will be provided to the project partners. Together they will analyse 2 000 carefully chosen Arabidopsis samples (two chips per sample, reference design) to have a first exploration of Arabidopsis "developmental and functional space". Samples will consist of biological replicates, some tissues and organs will be sampled even more extensively. The resulting data will be statistically analysed for quality and significance by ESAT, and subsequently submitted to the central ArrayExpress database at EBI. EBI will deliver specific CAGE ontology, and data submission pipelines. The compendium data will be annotated with pre-computed results, and thoroughly analysed for content and proof of gene function, as will be demonstrated in publications.

Deliverables

The duration of the project is three years. A total of 4 000 microarrays with up to 25 000 features will be produced over a period of 18 months (to be completed by the end of year 2. The partners will assemble 2 000 biological samples, and processing on microarrays will generate close to 100 000 000 data points. The reference sample used in all comparisons will be made publicly available. The first data will be produced by month 6, and data production will continue until month 30. All data will be analysed by the partners, and submitted for publication prior to releasing the compendium data to the scientific community. Data processing pipelines and pre-computed results will be released for public use. All data will become publicly available six months after CAGE finishes. The database will be maintained by the EBI.

Contacts

Coordinator

• VIB Dept. of Plant Systems Biology / BELGIUM

Participant

• Javier PAZ-ARES / Consejo Superior de Investigaciones Cientificas Dept. of Plant Molecular Genetics / SPAIN
• Vincent COLOT / INRA(URGV) Unité de Recherche en Génomique Végétale / FRANCE
• Max-Planck-Institute for Molecular Genetics Dept. Lehrach / GERMANY
• P J WEISBEEK / State University Utrecht Dept Molecular Cell Biology / NETHERLANDS
• Rishikesh BHALERAO / Swedish University of Agricultural Sciences Dept. of Forest Genetics and Plant Physiology
• Philippe REYMOND / University of Lausanne Institute of Ecology / SWITZERLAND
• Paul Van HUMMELEN / VIB Micro-Array Facility / BELGIUM