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KEGG Mapper


About KEGG Mapper

KEGG Mapper is a collection of tools for KEGG mapping: KEGG pathway mapping, BRITE mapping, and MODULE mapping. Two pathway mapping tools, "Search Pathway" and "Color Pathway", were made available from the beginning of the KEGG project. The naming of these tools was somewhat misleading since both involved searching and coloring procedures. The latter is now called "Search&Color Pathway" and a new "Color Pathway" is introduced for coloring of a selected pathway map (without searching).

Pathway mapping tools

Search Pathway - basic pathway mapping tool
  • Search against all pathway maps in one category (ko, org, etc.)
  • Multiple search objects may be specified in one line
  • Mapped objects are marked in red
Search&Color Pathway - pathway mapping tool with coloring options
  • Search against all pathway maps in one category (ko, org, etc.)
  • Each search object is specified in one line together with color attributes (background color and foreground color)
  • Mapped objects can be marked in any color
  • NCBI and UniProt identifiers may be used
Color Pathway - selected pathway map coloring tool
  • One selected pathway map is colored in multiple ways
  • Each object is specified in one line together with color attributes, i.e., multiple background and foreground colors in multiple columns
  • Results shown as multiple snapshots of image maps
  • When numerical values are given as attributes, they are displayed by gradation or by using WebGL graphics

Brite mapping tools

Search Brite - basic brite mapping tool
  • Search against all brite hierarchies in one category (ko+br or org+br)
  • Multiple search objects may be specified in one line
  • Mapped objects are marked in red
Search&Color Brite - brite mapping tool with coloring options
  • Search against all brite hierarchies in one category (ko+br or org+br)
  • Each search object is specified in one line together with color attributes (background color and foreground color)
  • Mapped objects can be marked in any color
Join Brite - tool to combine selected brite hierarchy and binary relation data
  • One selected brite hierarchy is combined with a relation file
  • It contains object-attributes relations
  • Results shown in additional columns or additional hierarchy levels

Module mapping tools

Search Module - basic module mapping tool
  • Search against all modules in one category (ko, org)
  • Multiple search objects may be specified in one line
  • Mapped objects are marked in red
Search&Color Module - module mapping tool with coloring options
  • Search against all module in one category (ko, org)
  • Each search object is specified in one line together with color attributes (background color and foreground color)
  • Mapped objects can be marked in any color

Mapping tools for KO annotation

Reconstruct Pathway - pathway mapping tool to assist genome annotation
  • Search against all pathway maps in the ko category
  • Search objects are user-defined genes annotated with K numbers
  • Mapped objects are marked in green for a single genome or in multiple colors (see: KEGG color codes) for multiple genomes
Reconstruct Brite - brite mapping tool to assist genome annotation
  • Search against all brite hierarchies in the ko category
  • Search objects are user-defined genes annotated with K numbers
  • Mapped objects are marked in green for a single genome or in multiple colors (see: KEGG color codes) for multiple genomes
Reconstruct Module - module mapping tool to assist genome annotation
  • Search against all modules in the ko category
  • Search objects are user-defined genes annotated with K numbers
  • Option to report complete modules or almost complete modules
  • Mapped objects are marked as green boxes

Taxonomy mapping tool

Map Taxonomy - taxonomy mapping tool to validate modules
  • Search taxonomy groups that contain a given K numbers, a given M number or a logical expression of K numbers and M numbers.
  • Report a highest-level taxonomy group by going up the hierarchy.

Concepts behind KEGG Mapper

KEGG PATHWAY and KEGG BRITE are the reference knowledge bases for biological interpretation of molecular datasets, especially large-scale datasets generated by high-throughput experimental technologies. KEGG Mapper will help to understand higher-level systemic functions, based on the set operation between the query data and the reference knowledge as shown below.

Query data Reference knowledge Tool
Objects
Object-atrributes relations1
Object-atrributes relations2
KEGG PATHWAY database
KEGG PATHWAY database
KEGG pathway map
Search Pathway
Search&Color Pathway
Color Pathway
Objects
Object-atrributes relations1
Object-atrributes relations3
KEGG BRITE database
KEGG BRITE database
Brite functional hierarchy
Search Brite
Search&Color Brite
Join Brite
Objects
Object-atrributes relations1
KEGG MODULE database
KEGG MODULE database
Search Module
Search&Color Module
Attributes are: 1 colors, 2 colors or numerical values, and 3 any attributes.

The query data may be a collection of molecular objects (genes, proteins, small molecules, etc.) or a more ordered set of object-attributes relations, such as:
  • orthologs and their presence in the genome (green boxes in KEGG pathways)
  • genes associated with up/down expression levels (green/yellow/red coloring)
  • genes associated with somatic mutation frequency (3D representation)

The "Reconstruct" tools are meant for assisting genome/metagenome annotations, where the user's gene list annotated with KO identifiers (such as the output of the BlastKOALA server) is used.

Query data Reference knowledge Tool
Gene-KO list KEGG PATHWAY database (KO)
KEGG BRITE database (KO)
KEGG MODULE database (KO)
Reconstruct Pathway
Reconstruct Brite
Reconstruct Module

In order to improve the KO annotation and the definition of KEGG modules, the new "Map Taxonomy" tool is introduced.

Query data Reference knowledge Tool
K number, M number or
expression of K/M numbers
Brite file for taxonomy Map Taxonomy

Release History

KEGG Mapper v2.4 released November 4, 2014
  • "Reconstruct Brite" tool has been updated to allow better integration with BlastKOALA and KAAS.
KEGG Mapper v2.3 released November 4, 2014
  • Another variant of "Map Taxonomy" tool is implemented in the BlastKOALA service to examine organism groups of query genomes/metagenomes.
KEGG Mapper v2.2 released July 1, 2014
  • "Taxonomy Checker" is introduced in the KEGG Annotation page as a variant of "Map Taxonomy" tool.
KEGG Mapper v2.1 released April 1, 2014
  • "Color Pathway 3D" is renamed to "Color Pathway WebGL" with updated features.
KEGG Mapper v2.0 released January 1, 2014
  • "Map taxonomy" is introduced to examine the organism groups assigned to a KEGG Orthology group (K number), a KEGG module (M number) or a definition of KEGG module (logical expression of K and M numbers).
KEGG Mapper v1.6 released October 1, 2013
  • "Reconstruct module" allows distinction of complete modules, as well as incomplete modules with only one or two blocks missing.
KEGG Mapper v1.6 released May 1, 2013
  • For selecting a pathway/brite/module type, the text box for entering a prefix code is used instead of the pulldown menu.
KEGG Mapper v1.5 released June 1, 2012
  • "Reconstruct Pathway/Brite" tools accept multiple genomes for comparison or combination.
KEGG Mapper v1.4 released April 1, 2012
  • "Reconstruct Pathway/Brite/Module" tools are made available.
  • "Color Pathway 3D" tool is released directly linking to KEGG Atlas 3D viewer.
KEGG Mapper v1.3 released July 1, 2011
  • "Color Pathway" accepts numerical data, which can be displayed either by gradation or by 3D representation.
KEGG Mapper v1.2 released September 20, 2011
  • "Search Module" is released.
KEGG Mapper v1.1 released June 1, 2011
  • "Color Pathway" is renamed to "Search&Color Pathway".
  • "Color Brite" is renamed to "Search&Color Brite".
  • New "Color Pathway" is released.
KEGG Mapper v1.0 released September 1, 2010
  • "Join Brite" tool is included in the existing collection of KEGG pathway mapping and BRITE mapping tools.


Last updated: November 6, 2014