MapMan

MapMan is a user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes.

MapMan was developed in cooperation with the group of Mark Stitt. For technical details, please contact Axel Nagel, for other questions, please contact Björn Usadel.

  • Version 3.6.0RC1 (19.06.2013) RELEASE CANDIDATE EXPERIMENTAL! (history)

    • New detail view on multiple data diagrams (right click, show details, show multiple graphs). Credits go to Elijah Myers of Virginia Tech
    • New type of installers which need Java to be installed
    • The search for publications concerning a given gene has been updated to use NCBI EUtils
    • Small changes to the data filter interface
    • Someusability enhancements
    • See NEW* installation instructions
  • Version 3.5.1 (19.11.2010) download (history)

    • Small BUGFIX release
    • BUGFIX: alignment options when editing pathways where blocked
    • BUGFIX: VennDIagramm4 misinterpretation of data due to typo
    • SMALL FEATURE: enabled data blocks to be displayed larger
    • SMALL FEATURE: Venn diagramms now have the sets names displayed
  • Download Version 3.1.0 (08.01.2010)   Version 3.1.0 from 29.01.2010 (history)
    • New Features: Venn diagram visualization
    • Requests related publications
    • New Interactive mouse overs for ease of use and additional information
    • Java 1.5 compliant for MacOSX users
    • For full details see Version History
    • See installation instructions
  • View Applicable License agreement
  • The Ultimate MapMan Install and Usage Guide MapManGuid.pdf * new .
  • Download MapMan pathway, mapping and sample data files.
    Get source data. Mapping files available in m02, text and xml format.
  • MapMan Forum:
    Post your questions, feature request and bug reports.
  • MapMan web-application: View some sample data sets.
  • MapMan annotation experts
  • References:
    • Reference: Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environment, 32: 1211-1229 cited 28 times (as of May 2012)
    • Reference:  Urbanczyk-Wochniak E, Usadel B, Thimm O, Nunes-Nesi A, Carrari F, Davy M, Blasing O, Kowalczyk M, Weicht D, Polinceusz A, Meyer S, Stitt M, Fernie AR (2005) Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: Effects of genetic and environmental alterations in energy metabolism in the leaf . Plant Molecular Biology 60:773-792 cited 49 times (as of May 2012).
    • Reference: Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S and M Stitt (2005), Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol. 138::1195-204. cited 150 times (as of May 2012).
    • Reference: Thimm O, Blaesing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY and M Stitt (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37(6):914-39.
      Selected as fast breaking paper in plant and animal sciences:
      http://www.esi-topics.com/fbp/2005/february05-OliverThimm.html
      cited 507 times (as of May 2012).
  • Adaptations:
    •  Rotter A, Camps C, Lohse M, Kappel C, Pilati S, Hren M, Stitt M, Coutos-Thévenot P, Moser C, Usadel B, Delrot S, Gruden K. (2009) Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine. BMC Plant Biol. 9:104. cited 11 times (as of May 2012).
    • Rotter A, Usadel B, Baebler S, Stitt M, Gruden K (2007) Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species. Plant Methods. 3:10 cited 9 times (as of May 2012).
    • Tellstrom V, Usadel B, Thimm O, Stitt M, Kuster H, Niehaus K (2007) The Lipopolysaccharide of Sinorhizobium meliloti Suppresses defense-associated Gene Expression in Cell Cultures of the Host Plant Medicago truncatula. Plant Physiol. 143:825-37 cited 41 times (as of May 2012).
    • Sreenivasulu Ne, Usadel Be, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ, Stitt M, Graner A, Wobus U (2008) Barley grain maturation and germination: Metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant Physiol., 146:1734-1761 cited 56 times (as of May 2012).
       
  • Acknowledgement: We would like to thank the TAIR team for their kind support in data annotation and good advices.

 

  • ToolTip with PubMed Info
  • Display time based Experiments
  • Show on Chromosome
  • PageMan Integration
  • Venn Diagram based on Annotation
Download: MapMan 3.5.1R2 Download: MapMan 3.5.1R2
Windows Installer( MapManLicense 3.0)
  MapManInst-3.5.1R2.exe
MacOSX Installer( MapManLicense 3.0)
  MapManInst-3.5.1R2.zip
Jar File( MapManLicense 3.0)
  MapManInst-3.5.1R2.jar
PDF Document 
  The Ultimate MapMan Install And Usage Guide.pdf
Linux Installer( MapManLicense 3.0)
  MapManInst-3.5.1R2.bin
Download: MapMan_3.6.0RC1 (HIGHLY EXPERIMENTAL) Download: MapMan_3.6.0RC1 (HIGHLY EXPERIMENTAL)
Windows Installer( MapManLicense 3.0)
  MapManInst-3_6_0RC1.exe
Jar File( MapManLicense 3.0)
  MapManInst-3_6_0RC1.jar
MacOSX Installer( MapManLicense 3.0)
  MapManInst-3_6_0RC1.dmg