A review of the new HGNC gene family resource

Abstract

The HUGO Gene Nomenclature Committee (HGNC) approves unique gene symbols and names for human loci. As well as naming genomic loci, we manually curate genes into family sets based on shared characteristics such as function, homology or phenotype. Each HGNC gene family has its own dedicated gene family report on our website, www.genenames.org . We have recently redesigned these reports to support the visualisation and browsing of complex relationships between families and to provide extra curated information such as family descriptions, protein domain graphics and gene family aliases. Here, we review how our gene families are curated and explain how to view, search and download the gene family data.

Fig. 1

Navigating through the gene family resource. Within the figure, ‘Cholinergic receptors’ was entered in to the search field and three results were returned. Clicking on the first result will navigate to the family ‘Cholinergic receptors’ (arrow a) whilst the second result navigates to the family ‘Cholinergic receptors, muscarinic’ (arrow b), a subset of ‘Cholinergic receptors’. It is possible to move through the hierarchy levels by clicking on the ‘A subset of’ link within the subset family (arrow c), by hovering the cursor over a family of interest within the ‘Gene family hierarchy map’ and clicking ‘View gene family’ within the tooltip (arrow d), or by clicking on a ‘Family contains the following subsets’ link (arrow e). Within a gene family report, it is possible to view the gene symbol report for each gene specified in the family by clicking on the approved symbol (arrow f). The resulting symbol report will have a ‘GENE FAMILY’ field within the top section of the page. It is possible for a gene to be a direct member of several families and if this is the case, they will all be listed within this field. Since the gene CHRM4 is a direct member of ‘Cholinergic receptors, muscarinic’, this family is listed in the CHRM4 symbol report and links back to the family (arrow g)

Fig. 2

Complex gene family hierarchies. Three hierarchical directed acyclic graphs (DAGs) which show the complex hierarchy levels centred around a highlighted family typical of many gene families within our resource. The gene family hierarchy map for ‘Serine/threonine phosphatases’ (a) follows a simple tree-like structure. However, the maps for the ‘Cholinergic receptors, muscarinic’ (b) and ‘HAD Asp-based protein phosphatases’ (c) families show that our maps are DAGs and do not always follow a tree-like structure

Fig. 3

A typical gene family report for a family at the lowest level within a hierarchy

Fig. 4

A typical gene family report for a family which contains subset families within a hierarchy