MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.

By O. Thimm, O. Bläsing, Y. Gibon, Axel Nagel, S. Meyer, Peter Krüger, Joachim Selbig, Lukas Müller, Seung Yon Rhee, Mark Stitt. The Plant Journal, 2004

3,246 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/32e48251d870f4c8cb9ae33fee9c8804f2a27b7f

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Citations in the corpus

PPDB, the Plant Proteomics Database at Cornell (2008, methodology): “We thank the curators of MapMan bin for providing us all MapMan bin assignments to Arabidopsis accessions.”
Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development (2008, methodology): “Genes were grouped according to annotations based on MapMan bins [96], Gene Ontology terms [25], and The Arabidopsis Information Resource [97] gene families, as well as information gleaned from the primary literature.”
Comparative metabolomics and transcriptomics of plant response to Tomato yellow leaf curl virus infection in resistant and susceptible tomato cultivars (2014, methodology): “Genes that show significantly (p \ 0.01; FC [3) change in R and S plants expression before and after TYLCV infection compared to untreated plants were subjected to functional categories analysis using MapMan (Thimm et al. 2004).”
Correlative GC-TOF-MS-based metabolite profiling and LC-MS-based protein profiling reveal time-related systemic regulation of metabolite–protein networks and improve pattern recognition for multiple biomarker selection (2005, background): “This cluster points to altered C/N partitioning, which has been hinted at previously in studies of transcriptional regulation (Gibon et al., 2004b; Thimm et al., 2004).”
Marker-Assisted Plant Breeding: Principles and Practices (2015, neutral): “, the SCAVENGER and the IMAGEANNOTATOR modules (Thimm et al. 2004).”
A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis (2010, methodology): “Results are the mean of three replicates, displayed on a log2 scale using MapMan software [35].”
Genome-Wide Reprogramming of Primary and Secondary Metabolism, Protein Synthesis, Cellular Growth Processes, and the Regulatory Infrastructure of Arabidopsis in Response to Nitrogen1[w] (2004, methodology): “The same subset of TPS genes is induced by sugar deprivation, and the same outlier is repressed (Thimm et al., 2004).”
Sucrose-Specific Induction of the Anthocyanin Biosynthetic Pathway in Arabidopsis[W] (2005, background): “…leaves accumulating high levels of soluble sugars and showing higher levels of expression of genes coding for anthocyanin biosynthesis enzymes (Lloyd and Zakhleniuk, 2004); these genes exhibit a very low expression level in sugar-depleted pgm leaves at the end of the night (Thimm et al., 2004).”
GMD@CSB.DB: the Golm Metabolome Database (2005, background): “The plant kingdom is believed to comprise in excess of 200 000 metabolites (Fiehn, 2002; Trethewey, 2004).”
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments (2006, methodology): “In the examples presented here, the mapping file is based on the MapMan ontology for Arabidopsis genes described in the user's manual and elsewhere [6,14].”