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Molecular database covering metabolite and transcript profiles of transgenic tomato lines altered in flavonoid biosynthesis

Changes of transcripts and metabolites have been measured in transgenic lines altered in flavonoid metabolism by different partners of the PROFOOD consortium. All data have been combined and stored in a database located at the MPI-Golm (Partner 7. Genes used encode proteins invovled in the transport of precursors across the plastid envelope membrane, and transcription factors involved in the regulation of the expression of genes involved in flavanoid synthesis.

In addition, a data visualisation software tool has been developed, which allows tomato expression data to be visualised in a user-driven manner on diagrams or maps. The MapMan visualization software was developed previously for Arabidopsis thaliana transcript and metabolite profiling. It offers the possibility to paint out microarray or metabolite profiling experiments onto diagrams of pathways or processes, and visualize the responses of gene expression in a biological context at either a gene for gene level or at different hierarchical levels of the functional categorisation system. This plant specific ontology is a key element of MapMan. The principle of the MapMan ontology is a hierarchical “BIN”-based structure. Each BIN comprises items of similar biological function e.g. glycolysis, and can be further split into subBINs corresponding to submodes of the biological function. It presently contains over 700 hierarchical categories. In contrast to the GO ontology (The Gene Ontology Consortium, 2000), the MapMan BIN structure minimizes the redundancy between BINs. The hierarchical structure is reflected in its “BINCode” by separating dots similar to EC numbers. Thus BIN 1 (photosynthesis) can, for example, be subdivided to 1.1 (Photosynthesis.light reaction) and 1.2 (Photosynthesis.Calvin cycle). This allows the relationship between subBINs and BINS to be deduced immediately from the name of the BIN as well as from its numerical BINCode. A very important goal was to extend this software platform to allow it to be applied to crop plants, which will allow knowledge generated by analysis of the model system Arabidopsis to be used to support crop genomic research. We have developed a classification of the spots represented on the tomato TOM1 array according to the MapMan ontology. This allows the software systems developed for Arabidopsis to be used for the visualisation system of tomato and other Solanaceous transcript profiling data.

A similar approach has been taking to display metabolite data on diagrams of metabolic pathways.

The results have been accepted for publication.

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Reported by

Max Planck Society
Max Planck Institute oif Molecular Plant Physiology, Am Muehlenberg 1 Golm
14474 Potsdam
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