MapMan desktop application

The MapMan desktop application displays plant protein function annotation results combined with gene expression data onto diagrams of metabolic pathways or other processes. This requires an installation of the MapMan desktop application (available for MS Windows, MacOS and Linux) on a local computer (see download & installation).

Display gene expression and protein annotation in a diagram

To display protein function annotations combined with gene expression data for a certain set of protein sequences, the installed MapMan desktop application needs:

• protein function annotations for the sequences
  submit the sequences to the online protein function annotation tool Mercator4 and download the annotation results

  Example table from a Mercator4 annotation result file

• gene expression data
  provide a gene expression count table of the sequences (further details on the format are available in the MapMan desktop application user guide)

  It is important that protein/gene identifiers are identical (case sensitive !) in both the Mercator4 annotation result file and the gene expression file (green columns in example tables).

  Example for a gene expression count table

• pathway diagram
  provide a pathway diagram (see diagrams).

Publications & Contact

• Usadel et al. (2009)
  A guide to using MapMan to visualize and compare omics data in plants: a case study in the crop species maize.
  Plant Cell Environ. 2009 Sep, 32(9): 1211-1229.
• Usadel et al. (2005)
  Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses.
  Plant Physiol. 2005 Jul, 138(3): 1195-1204.
• Thimm et al. (2004)
  MapMan: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
  Plant J. 2004 Mar, 37(6): 914-939.

For any questions, please feel free to contact us (plabipd@fz-juelich.de).

• Install on Linux, Windows or MacOS

  • download the Java archive (.jar) file for the MapMan desktop application MapMan-3.7.1-jar-with-dependencies.jar
  • verify that a Java Virtual Machine (JVM) is installed (optionally check by java -version)
  • run the MapMan application: java -jar MapMan-3.7.1-jar-with-dependencies.jar

Diagrams for the MapMan desktop application

The MapMan desktop application requires a diagram that illustrates the pathway or process to be visualized. Each diagram consists of a pathway image file (SVG-format) and an extra protein/gene mapping file (XML-format).
The X4.7 diagrams can only be used with results from Mercator4 version 7, not with results from other Mercator4 versions or from Mercator v.3.6.

Basic diagrams for annotations from Mercator4 v.7

Download a diagram from the lists below and unzip it (the .zip file contains both the pathway image file and the protein mapping file). The list contains the currently available diagrams for Mercator4 and will be extended.

Available basic diagrams

• X4.7 Metabolism overview
• X4.7 Photosynthesis
• X4.7 Cellular respiration
• X4.7 Carbohydrate metabolism
• X4.7 Amino acid metabolism
• X4.7 Lipid metabolism
• X4.7 Nucleotide metabolism
• X4.7 Coenzyme metabolism
• X4.7 Polyamine metabolism
• X4.7 Secondary metabolism
• X4.7 Redox homeostasis
• X4.7 Chromatin organisation
• X4.7 Vesicle trafficking

Custom-made diagrams for annotations

User can create an individual pathway diagram to display their own data. Use your favorite image software to create the background image file. Choose a version of Mercator annotations and generate the extra protein mapping file within the MapMan desktop application by using annotation result files from the chosen Mercator version. Some custom-made diagrams are publicly available.

Available custom-made diagrams

• X4.7 Jasmonic acid biosynthesis
• X4.7 Gibberellic acid biosynthesis
• X4.7 Tetrapyrrole biosynthesis
• X4.7 Tocopherol biosynthesis
• X4.7 Monolignol biosynthesis

Diagrams for the MapMan desktop application

The MapMan desktop application requires a diagram that illustrates the pathway or process to be visualized. Each diagram consists of a pathway image file (SVG-format) and an extra protein/gene mapping file (XML-format). There are different diagram sets for Mercator4 annotations and for Mercator v.3.6 annotations available.
The X4.6 diagrams can only be used with results from Mercator4 version 5, not with results from other Mercator4 versions or from Mercator v.3.6.

Basic diagrams for annotations from Mercator4 v.6

Download a diagram from the lists below and unzip it (the .zip file contains both the pathway image file and the protein mapping file). The list contains the currently available diagrams for Mercator4 and will be extended.

Available basic diagrams for Mercator4 v.6 annotations

• X4.6 Metabolism overview
• X4.6 Photosynthesis
• X4.6 Cellular respiration
• X4.6 Carbohydrate metabolism
• X4.6 Amino acid metabolism
• X4.6 Lipid metabolism
• X4.6 Nucleotide metabolism
• X4.6 Coenzyme metabolism
• X4.6 Polyamine metabolism
• X4.6 Secondary metabolism
• X4.6 Redox homeostasis
• X4.6 Chromatin organisation
• X4.6 Vesicle trafficking

Custom-made diagrams for annotations

User can create an individual pathway diagram to display their own data. Use your favorite image software to create the background image file. Choose a version of Mercator annotations and generate the extra protein mapping file within the MapMan desktop application by using annotation result files from the chosen Mercator version. Some custom-made diagrams are publicly available.

Available custom-made diagrams for Mercator4 v.6 annotations

• X4.6 Jasmonic acid biosynthesis
• X4.6 Gibberellic acid biosynthesis
• X4.6 Tetrapyrrole biosynthesis
• X4.6 Tocopherol biosynthesis
• X4.6 Monolignol biosynthesis

Diagrams for the MapMan desktop application

The MapMan desktop application requires a diagram that illustrates the pathway or process to be visualized. Each diagram consists of a pathway image file (SVG-format) and an extra protein/gene mapping file (XML-format). There are different diagram sets for Mercator4 annotations and for Mercator v.3.6 annotations available.
The X4.3 diagrams can only be used with results from Mercator4 version 3, not with results from other Mercator4 versions or from Mercator v.3.6.

Basic diagrams for annotations from Mercator4 v.3

Download a diagram from the lists below and unzip it (the .zip file contains both the pathway image file and the protein mapping file). The list contains the currently available diagrams for Mercator4 and will be extended.

Available basic diagrams for Mercator4 v.3 annotations

• X4.3 Photosynthesis
• X4.3 Cellular respiration
• X4.3 Carbohydrate metabolism
• X4.3 Amino acid metabolism
• X4.3 Lipid metabolism
• X4.3 Nucleotide metabolism
• X4.3 Coenzyme metabolism
• X4.3 Polyamine metabolism
• X4.3 Secondary metabolism

Custom-made diagrams for annotations

User can create an individual pathway diagram to display their own data. Use your favorite image software to create the background image file. Choose a version of Mercator annotations and generate the extra protein mapping file within the MapMan desktop application by using annotation result files from the chosen Mercator version. Some custom-made diagrams are publicly available.

Available custom-made diagrams for Mercator4 v.3 annotations

• X4.3 Jasmonic acid biosynthesis
• X4.3 Gibberellic acid biosynthesis
• X4.3 Tetrapyrrole biosynthesis
• X4.3 Tocopherol biosynthesis
• X4.3 Monolignol biosynthesis

Diagrams for the MapMan desktop application

The MapMan desktop application requires a diagram that illustrates the pathway or process to be visualized. Each diagram consists of a pathway image file (SVG-format) and an extra protein/gene mapping file (XML-format). There are different diagram sets for Mercator4 annotations and for Mercator v.3.6 annotations available.
The MapMan v.3 diagrams can only be used with results from Mercator v.3.6, not with results from Mercator4 versions.

Basic diagrams for annotations from Mercator v.3.6

Download a diagram from the lists below and unzip it (the .zip file contains both the pathway image file and the protein mapping file). The list contains the currently available diagrams for Mercator4 and will be extended.

Available basic diagrams for Mercator v.3.6 annotations

• Core_metabolism_overview

Custom-made diagrams for annotations

User can create an individual pathway diagram to display their own data. Use your favorite image software to create the background image file. Choose a version of Mercator annotations and generate the extra protein mapping file within the MapMan desktop application by using annotation result files from the chosen Mercator version. Some custom-made diagrams are publicly available.

Available custom-made diagrams for Mercator v.3.6 annotations

• Ribosomal_proteins_overview
• Prokaryotic_Ribosome_LSU_assembly
• Prokaryotic_Ribosome_SSU_5S_branch_assembly
• GA_synthesis_later_stages
• Coenzyme_A_Biosynthesis
• ABA_metabolism
• Plant_glycolysis
• Protein_glycosylation