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
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
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
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 |
KEGG MODULE database |
Search 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 v1.2 released July 1, 2011
- "Color Pathway" accepts numerical data, which can be displayed either by gradation or by 3D representation.
KEGG Mapper v1.r 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: September 20, 2011
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