KEGG Modules
KEGG MODULE is a collection of manually defined functional units, termed KEGG modules, used for annotation and biological interpretation of sequenced genomes. Each module is identified by the M number that corresponds to a set of K numbers (KO identifiers). There are four types of KEGG modules:
- pathway modules – representing tight functional units in KEGG metabolic pathway maps, such as M00002 (Glycolysis, core module involving three-carbon compounds)
- structural complexes – often forming molecular machineries, such as M00072 (Oligosaccharyltransferase)
- functinal sets – for other types of essential sets, such as M00360 (Aminoacyl-tRNA synthases, prokaryotes)
- signature modules – as markers of phenotypes, such as M00363 (EHEC pathogenicity signature, Shiga toxin)
The entire list of KEGG modules can be viewed from the BRITE hierarchy file:
- KEGG modules
Each M number entry is defined by the Boolean-like expression for the combination of K numbers. Notations for this definition include:
- space delimited items for pathway elements
- comma separated items in parentheses for alternatives
- plus sign to define a complex
- minus sign for an optional item
Phenotype Inference
A single M number or a combination of M numbers can be used for characterizing phenotypic features encoded in the genome. For example, the BTX (benzen, toluene, and xylene) degradation capacity can be seen from the following diagram where M numbers are linked to the ortholog tables indicating in which KEGG organisms modules are complete.
It is interesting to note that KEGG pathway modules often correspond to reaction modules extracted from purely chemical properties as summarized in the following BRITE hierarchy file.
- KEGG reaction modules
The above example can be rewritten in terms of the reaction modules.
|
benzene |
— RM006 → |
catechol |
| toluene |
— RM003 → |
benzoate |
— RM005 → |
catechol |
— RM009 → |
meta-cleavage |
|
— RM008 → |
ortho-cleavage |
| xylene |
— RM003 → |
methyl-
benzoate |
— RM005 → |
methyl-
catechol |
— RM009 → |
meta-cleavage |
|
— RM008 → |
ortho-cleavage |
Module Maps
KEGG modules are associated with graphical diagrams called module maps. For example, M00002 represents glycolysis core module involving three-carbon compounds and its organism specific module can be selected from the pop-up menu or directly specified in the form of hsa_M00002. While KEGG pathway maps are all manually drawn, KEGG module maps are computationally generated from the text definition describe above. There is also a difference of how organism-specific versions are generated. Organism specific modules are generated only when consituent components are present in the genome.
Module Mapping
The KEGG Mapper interface allows KEGG MODULE mapping in a similar way to KEGG PATHWAY mapping.
Ortholog Table
The ortholog table is a useful tool to check completeness and consistency of genome annotations. It shows currently annotated genes in individual genomes for a given set of K numbers, together with coloring of adjacent genes (operon-like structures) on the chromosome. Each KEGG module contains a link to the corresponding ortholog table.
Taxonomy Mapping
Each KEGG module also contains a link to KEGG taxonomy mapping, which indicates the presence or absence of the module in all KEGG organisms under a taxonomic classification.
Last updated: April 1, 2013
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