<scp>mapman</scp>: a user‐driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes

Plant Journal - Tập 37 Số 6 - Trang 914-939 - 2004
Oliver Thimm1, Oliver E. Bläsing1, Yves Gibon1, Axel Nagel2, Svenja Meyer2, Peter Krüger1, Joachim Selbig1, Lukas Niklaus Müller3, Seung Y. Rhee3, Mark Stitt1
1Max Planck Institute for Molecular Plant Physiology, Golm, Germany
2RZPD German Resource Centre for Genome Research, Heubnerweg 6, D‐14059 Berlin, Germany, and
3TAIR, The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institution of Washington, Stanford, Germany

Tóm tắt

Summary mapman is a user‐driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. SCAVENGER modules assign the measured parameters to hierarchical categories (formed ‘BINs’, ‘subBINs’). A first build of transcriptscavenger groups genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cellular processes. metabolitescavenger groups hundreds of metabolites into pathways or groups of structurally related compounds. An imageannotator module uses these groupings to organise and display experimental data sets onto diagrams of the users' choice. A modular structure allows users to edit existing categories, add new categories and develop SCAVENGER modules for other sorts of data. mapman is used to analyse two sets of 22K Affymetrix arrays that investigate the response of Arabidopsis rosettes to low sugar: one investigates the response to a 6‐h extension of the night, and the other compares wild‐type Columbia‐0 (Col‐0) and the starchless pgm mutant (plastid phosphoglucomutase) at the end of the night. There were qualitatively similar responses in both treatments. Many genes involved in photosynthesis, nutrient acquisition, amino acid, nucleotide, lipid and cell wall synthesis, cell wall modification, and RNA and protein synthesis were repressed. Many genes assigned to amino acid, nucleotide, lipid and cell wall breakdown were induced. Changed expression of genes for trehalose metabolism point to a role for trehalose‐6‐phosphate (Tre6P) as a starvation signal. Widespread changes in the expression of genes encoding receptor kinases, transcription factors, components of signalling pathways, proteins involved in post‐translational modification and turnover, and proteins involved in the synthesis and sensing of cytokinins, abscisic acid (ABA) and ethylene revealing large‐scale rewiring of the regulatory network is an early response to sugar depletion.

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Plant Journal

Tập 37 Số 6

914-939

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