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Functional Coupling and Chromosomal Clusters

Two genes are considered functionally coupled if they tend to be placed near each other in genomes belonging to diverse species. This proximity indicates that the genes perform related functions: the term functional coupling reflects the notion that the two genes function together.

The diagram below shows a section of the Campylobacter jejuni genome centered on fig|360108.3.peg.1041, which has the functional role ATP synthase delta chain. The orange gene right next to it is fig|360108.3.peg.1042, which has the role ATP synthase B chain.

Genome Fragment showing a cluster of the ATP synthase delta chain in Campylobacter jejuni

These genes are considered functionally coupled because they appear together in five other genomes, as shown below.

Evidence of functional coupling for two ATP synthase proteins in Campylobacter jejuni

The red and orange genes in these diagrams are not absolutely identical, but they are similar enough to be considered close relatives.

On the Genome Viewer Annotation Page, genes that are functionally coupled to the focus gene will have a number in the FC column of the Tabular Region Display. In the screen fragment below, there is a 5 in the functional coupling column for fig|360108.3.peg.1402, indicating that its proximity to fig|360108.3.peg.1401 is conserved in five other organisms. Clicking on the number will take you to a page listing the five gene pairs that demonstrate the functional coupling.

The genes functionally coupled to the focus gene are called its conserved neighbors. A group of conserved neighbors that appears in more than four genomes is called a chromosomal cluster. In the tabular region display shown above, you can use the cluster button to see the chromosomal cluster of a specific gene.

A more formal treatment of this topic can be found in the paper The use of gene clusters to infer functional coupling, which describes a method for computing functional coupling of features using conserved gene clusters.