Content

• Description
• Disclaimer
• Input
• Options
• Output
• Email
• Next steps panel
• Web service
• Standalone tool
• Related tools
• Literature

Description

The KEGG network provider allows the construction of bipartite metabolic networks specific to a set of organisms. The networks are constructed from KEGG KGML files. Compounds and reactions are represented as separate node sets.
It is also possible to filter the network in order to exclude certain reactions, compounds or reactant pair classes. In addition, compounds and reactions in the constructed networks can be annotated with their label or EC number.
Note that KGML files do not list the side compounds of reactions. These will consequently be missing from the constructed metabolic network as well.

Disclaimer

For the use of KEGG PATHWAY data, see the KEGG licence

Input

• KEGG organism identifiers
  Organisms present in KEGG can be specified by their KEGG abbreviation or full species name as given in KEGG. Note that the species name may also include the strain, e.g. Bacillus anthracis A2012. If you want to specify more than one organism, you can separate organism identifiers by '/' (e.g. eco/Saccharomyces cerevisiae). Note that the reference pathways can be requested with 'reference'. The reference pathways merge all organism-specific pathways. The list of KEGG organisms and their abbreviations in KEGG is available here.
• KEGG organism file
  Instead of or in addition to specifying organisms manually, a file with KEGG organisms can be up-loaded. The file contains one organism (KEGG identifier or species name) on each line. Comment lines in the file should be preceded by '#'.
• KEGG reactions
  In addition to or instead of KEGG organisms, KEGG reactions can be specified. The graph will be constructed from the specified reactions. The reactions should be separated by '/' (e.g. R00015/R00551).
• KEGG reaction file
  Instead of or in addition to manually specifying KEGG reactions, a file can be provided, which contains one KEGG reaction by line. Comment lines in this file should be preceded by '#'.

Options

• Exclusion of KEGG compounds
  Optionally, a set of KEGG compounds can be excluded from the network to be constructed. KEGG compound identifiers should be separated by '/' (e.g. C00001/C00002/C00010).
• Exclusion of KEGG reactions
  Optionally, a set of KEGG reactions can be excluded from the network to be constructed. KEGG compound identifiers should be separated by '/' (e.g. R000259/R04453).
• Exclusion of KEGG RPAIR classes
  Optionally, certain RPAIR classes can be excluded from network construction. Reactant pairs (RPAIRS) in KEGG are divided in five classes: main, trans, cofac, ligase and leave. Excluding ligase or leave reactant pairs may improve path finding accuracy. If you want to exclude more than one RPAIR class, separate them by '/' (e.g. leave/ligase/cofac).
• Directed network
  By default, undirected metabolic networks are constructed. However, in metabolic pathfinding, it is useful to represent reactions by separate nodes for the forward and reverse direction respectively. If "directed network" is selected, the constructed network is directed, but contains for each forward reaction direction its reverse.
• RPAIR network
  For the description of RPAIR networks see the metabolic Pathfinder help. If "RPAIR network" is selected, a metabolic network containing reactant pairs instead of reactions is constructed.
• Reaction treatment
  By default, irreversible reactions are converted into reversible ones. If you would like to keep the irreversible reactions, select this option. Note that it will only be effective in directed networks and that a reaction might be carried out in different directions in different organisms (resulting in a reversible presentation of this reaction after merging of the metabolic networks of these organisms).
• Attributes
  By default, the following attributes are set:
  
  • ObjectType: The ObjectType allows to differentiate between reaction and compound nodes.
  • ExclusionAttribute: Forward and reverse direction of the same reaction share a common value for the ExclusionAttribute, which allows to treat them as mutually exclusive.
  • ENZYME (reaction network only): Enzymes catalysing the reaction as provided in the KGML file. Note that because of the N:N relationship between reaction and reactant pair, it is not straightforward to set this attribute on reactant pairs. Note also that the reference pathways do not provide enzyme names, as they are organism-independent.
  • Exclusion.Group (RPAIR network only): Its value is a set of all reactant pairs sharing a common reaction with the given reactant pair.
  • RPAIRS.Linkage.Type (RPAIR network only): It has as its value the set of RPAIR classes to which a given reactant pair - compound interaction belongs.
  Optionally, the following attributes can be set in addition:
  Compounds
  
  • Name: The name of a KEGG compound.
  • Formula: The formula of a KEGG compound.
  Reactions
  
  • Equation (reaction network only): The equation of a KEGG reaction.
  • EC numbers: The EC numbers associated to a KEGG reaction or reactant pair.
  Note that the optional attributes are set with the help of a relational database storing KEGG data, as the KGML files do not provide compound names, formulas or reaction equations. The reaction equation is especially useful to see the side compounds, which are omitted in the KGML files. EC numbers are also set with the help of this database rather than from the KGML files, since the relationship between reactant pairs and EC numbers is not contained in the KGML files.

Output

Network format
The network can be constructed in different formats. See the metabolic Pathfinder help for details. Warning: The next step panel is only available for gml and tab-delimited graph formats. However, the next step panel allows to convert the network in dot or VisML.

Email

You can optionally specify an email address, so KEGG network provider results can be sent to you by email. This is recommended if you specify a large number of organisms. If you leave the email field empty, results will be displayed in the browser.

Next steps panel

The next steps panel allows you to input the result of KEGG network provider into one of the listed tools without copy-pasting the result into that tool. The next steps panel will only appear if you choose gml or tab-delimited as network format.

Web service

KEGG network provider does not use the usual RSAT Web Service address! Check the NeAT web services page.

Standalone tool

A stand alone version of KEGG network provider is available with the RSAT distribution.

Related tools

This list provides links to tools for the visualization/extraction/analysis of KEGG metabolic networks:
• KEGGgraph parse KEGG PATHWAY in R and Bioconductor (R package)
• Yanasquare construct metabolic networks from KEGG for elementary mode analysis (stand alone)
• Pathway Hunter Tool analyze topology and obtain organism-specific KEGG networks (web tool)
• KGML-ED navigate, visualize and edit pathways in KGML format (Java web start)
• metaSHARK navigate and visualize KEGG networks and map gene expression data on them (web tool)
• iPATH browse and export organism-specific KEGG pathway maps (web tool)

Literature

1. Kanehisa, M. et al. (2008). KEGG for linking genomes to life and the environment. Nucleic Acids Research 36, D480-D484.

For information, contact Karoline Faust