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 - advanced pathway mapping tool

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 and optionally by 3D representation as well

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

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 - advanced brite mapping tool

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 - selected brite hierarchy manipulation tool

One selected brite hierarchy is combined with a relation file
It contains object-attributes relations
Results shown in additional columns or additional hierarchy levels

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

Module mapping tool

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 - advanced module mapping tool

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

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 only the complete modules with all constituents annotated
Mapped objects are marked as green boxes

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 Gene-KO list	KEGG PATHWAY database KEGG PATHWAY database Single KEGG pathway map KEGG PATHWAY database (KO)	Search Pathway Search&Color Pathway Color Pathway / Color Pathway 3D Reconstruct Pathway
Objects Object-atrributes relations¹ Object-atrributes relations³ Gene-KO list	KEGG BRITE database KEGG BRITE database Single Brite functional hierarchy KEGG BRITE database (KO)	Search Brite Search&Color Brite Join Brite Reconstruct Brite
Objects Object-atrributes relations¹ Gene-KO list	KEGG MODULE database KEGG MODULE database KEGG MODULE database (KO)	Search Module Search&Color Module Reconstruct 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)

Release History

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: May 1, 2013