About KEGG Mapper
KEGG Mapper is a collection of tools for KEGG mapping including popular KEGG pathway mapping, JOIN BRITE operations and MODULE completeness checks. Historically, two basic tools of "Search Pathway" (currently, Search) and "Search&Color Pathway" (currently, Color) were introduced at the beginning of the KEGG project. As the KEGG database contents expanded, so did the mapping tools [1,2].The current version 5 of KEGG Mapper released in July 2021 consists of four tools: Reconstruct, Search, Color and Join. Since October 2023 these tools are tightly integrated with KEGG pathway map viewer and Brite hierarchy viewer, so that the final steps of mapping are processed on the client side.
See also: Map coloring GUI and Map coloring URL in KEGG Web Apps.
KEGG Mapper tools
There are four KEGG Mapper tools as summarized below.
Reconstruct is the basic mapping tool used for linking KO annotation (K number assignment) data to KEGG pathway maps, BRITE hierarchies and tables, and KEGG modules.
Search is the traditional tool for searching mapped objects in the user's dataset and mark them in red.
Color is another traditional tool for searching mapped objects in the user's dataset and mark them in any combination of background and foreground colors. This tool now applies only to KEGG pathway maps. Use the Join tool for coloring of Brite hierarchies.
Join is a tool to combine a Brite hierarchy file and a binary relation file, effectively adding a new column to the hierarchy file.
Query data must be prepared differently for different tools as shown below.
Reconstruct is the basic mapping tool used for linking KO annotation (K number assignment) data to KEGG pathway maps, BRITE hierarchies and tables, and KEGG modules.
Search is the traditional tool for searching mapped objects in the user's dataset and mark them in red.
Color is another traditional tool for searching mapped objects in the user's dataset and mark them in any combination of background and foreground colors. This tool now applies only to KEGG pathway maps. Use the Join tool for coloring of Brite hierarchies.
Join is a tool to combine a Brite hierarchy file and a binary relation file, effectively adding a new column to the hierarchy file.
| Tool | Search mode | Target database | Query data (KEGG identifier) |
| Reconstruct | Reference | Pathway Brite hierarchy Brite table Module |
K number |
| Search | Reference | Pathway Brite hierarchy Brite table Module |
K/R/EC number C/G/D/H number KEGG organism code |
| hsa | Pathway (hsa) Brite hierarchy (hsa) Module (hsa) Network Disease |
Human gene identifier C/G/D number |
|
| other org1 | Pathway (org) Brite hierarchy (org) Module (org) |
Gene identifier C/G/D number |
|
| Color | Reference | Pathway | K/R/EC number C/G/D number |
| org1 | Pathway (org) | Gene identifier C/G/D number |
|
| Join | Reference | Brite hierarchy Brie table |
K number C/G/D/H number KEGG organism code |
org1 three- or four-letter organism code
Query data must be prepared differently for different tools as shown below.
| Tool | Data format | Remark |
| Reconstruct | K number in the second column of each line The first column may be used for user's gene ID |
Same as BlastKOALA output |
| Search | Free format - KEGG identifiers separated by whitespace characters (space, tab, newline) |
Filter option available |
| Color | KEGG identifier in the first column of each line Optional color specification in the second column (background color and foreground color) |
|
| Join | KEGG identifier in the first column of each line Any attribute in the second column |
Other tools
Convert ID - Conversion of outside identifiers to KEGG identifiers
- Accept NCBI-GeneIDs, NCBI-ProteinID and UniProt accession for conversion into KEGG GENES ID
- Accept query amino acid sequence data in FASTA format
- Compare against a small subset of KEGG GENES database using BlastKOALA
- Annotation (KO assignment) result linked to the Reconstruct tool
Taxonomy mapping tool
The Taxonomy mapping tool is a special purpose mapping tool based on the KEGG Mapper Join function. It is designed to integrate taxonomic distributions of KOs and modules with phenotypic features.
References
- Kanehisa, M. and Sato, Y.; KEGG Mapper for inferring cellular functions from protein sequences. Protein Sci. 29, 28-35 (2020). [pubmed] [pdf]
- Kanehisa, M., Sato, Y., and Kawashima, M.; KEGG mapping tools for uncovering hidden features in biological data. Protein Sci. 31, 47-53 (2022). [pubmed] [doi]
Last updated: April 1, 2024