Extracting the HGNC gene group/family ontology.
- A review of the new HGNC gene family resource
Kristian A Gray, Ruth L Seal, Susan Tweedie, Mathew W Wright, Elspeth A Bruford
Human Genomics (2016-02-03) https://doi.org/bw6j
DOI: 10.1186/s40246-016-0062-6 · PMID: 26842383 · PMCID: PMC4739092 - The importance of being the HGNC
Elspeth A Bruford, Bryony Braschi, Liora Haim-Vilmovsky, Tamsin EM Jones, Ruth L Seal, Susan Tweedie
Human Genomics (2022-11-15) https://doi.org/grzk3p
DOI: 10.1186/s40246-022-00432-w · PMID: 36380364 · PMCID: PMC9664783 - https://www.genenames.org/help/genegroup/
- HGNC/hgnc-gene-family-mapper#2
- https://bioregistry.io/registry/hgnc.genegroup
From Gray et al 2016:
Family hierarchies can form complex structures, e.g. ‘Serine/threonine phosphatases’ which belong to the ‘Protein phosphatases’ family are themselves split into subset families; in this case, the hierarchy model looks like a tree (Fig. 2a). However, a family could be part of more than one hierarchy, for instance the family ‘Cholinergic receptors, muscarinic’ is a subset family of both ‘Amine receptors’ and ‘Cholinergic receptors’ (Fig. 2b). In other cases, a family can be divided into multiple subset families and a particular family could have more than one preceding and succeeding family, e.g. ‘HAD ASP-based protein phosphatases’ family in Fig. 2c. Due to these complexities, it is better to visualise the hierarchies as directed acyclic graphs (DAGs). ...
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
From Bruford et al 2022:
HGNC further provides a large set of over 1600 “gene groups”—sets of genes grouped by homology, shared function, complex membership, etc. One gene can belong to many groups, such as the AKAP13 gene which is in 5 groups, including the diverse “Dbl family Rho GEFs”, “Minor histocompatibility antigens” and “MicroRNA protein coding host genes”. Many groups have a dedicated “specialist advisor”, a community expert who provides advice on naming within that family.