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KEGG Syntax

Linking positional correlation of genes to functional correlation

KEGG Syntax

KEGG Syntax is a new resource for analyzing conserved gene orders or conserved synteny under appropriate levels of taxonomic ranks. Such conserved gene sets with positional correlations along the chromosome is an addition to the existing datasets of conserved genes (KOs) and conserved gene sets of functional correlations (KEGG modules) in pathways. KEGG Syntax aims to link positional correlations of genes to functional correlations. KEGG Syntax is tightly integrated with Genome browser, which is one of the KEGG Web Apps.

Conserved genes

In KEGG conserved genes are represented by KOs (KEGG Orthology groups) for both cellular organisms and viruses. KOs are manually defined from functionally characterized genes and proteins in specific organisms, but they are expanded to other organisms based on sequence similarity.

For viruses, VOGs (virus ortholog groups) are defined fully computationally to supplement low assignment of KOs.

Conserved gene orders

As the result of KO and VOG assignments to genes in the genome, similar gene orders can be found by a sequence alignment method by considering the genome as a sequence of KO identifiers or VOG identifiers. A new genome comparison method has been developed using the Goad-Kanehisa algorithm, enabling the development of the KEGG Syntax resouce.

Conserved functional units of genes

KEGG modules are examples of conserved functional units of genes. They are manually defined sets of enzyme genes that are involved in successive reactions steps in conserved subpathways of metabolic pathways. They sometimes contain positionally correlated genes, as in operon structures of prokaryotic genomes.

Last updated: April 1, 2024