Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses1

By Björn Usadel, Axel Nagel, O. Thimm, Henning Redestig, O. Blaesing, N. Palacios-Rojas, Joachim Selbig, Jan Hannemann, M. Piques, D. Steinhauser and 6 more. Plant Physiology, 2005

611 citations recorded by the source corpus.

MapMan is a user-driven tool that displays large genomics datasets onto diagrams of metabolic pathways or other processes. Here, we present new developments, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, the incorporation of statistics packages, and extensions of the software to incorporate more biological information including visualization of coresponding genes and horizontal searches for similar global responses across large numbers of arrays.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e4c2d1f7614004702f3c8fe7e6b9f76c10571186

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Citations in the corpus

Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “de/projects/MapMan/) according to the standard protocol (Thimm et al., 2004; Usadel et al., 2005).”
PHO2, MicroRNA399, and PHR1 Define a Phosphate-Signaling Pathway in Plants1[W][OA] (2006, background): “Transcripts for some of these genes cannot be reliably measured using the Affymetrix ATH1 genechip due to low expression, nonspecific probe sets (Usadel et al., 2005), or absence from the array.”
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community (2019, background): “Name to ID conversion Open [41] BiofOmics • Transcriptomics • Proteomics • Metabolomics Biofilm - Experiment library - Data depository Open [113] BioCyc/MetaCyc • Genomics • Proteomics • Metabolomics Unspecified - Online encyclopedia of metabolism - Predicted metabolic pathways in sequenced genomes ”
Sugars and Circadian Regulation Make Major Contributions to the Global Regulation of Diurnal Gene Expression in Arabidopsis[W][OA] (2005, methodology): “…4 and 5 online) were also generated to display the amplitude of the diurnal change and the timing of the maximum on a gene-for-gene basis in the visualization tool MapMan (Thimm et al., 2004; Usadel et al., 2005; for web-based and downloadable versions, see http:// gabi.rzpd.de/projects/MapMan/).”
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments (2006, methodology): “The analysis algorithm for the Wilcoxon test has been described earlier [6].”
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update (2009, methodology): “A new feature implemented is the annotation of each protein based on its biological function as classiﬁed by MAPMAN (17).”