Human and Mouse Orthologous Gene Nomenclature (HUMOT)
This is an archived page that is no longer updated
We make every effort to reduce interspecies nomenclature confusion by assigning the same gene symbol to orthologous genes. Orthologs are genes in different species that derive from a common ancestor, and generally share the same function. Hence, comparative genomics frequently provides an insight into the putative functions of genes in different species. The utility of standardised orthologous gene names is perhaps one of the strongest arguments for approved nomenclature and cooperation between nomenclature committees. Without this resource the analysis of comparative maps would be made far more difficult.
The HUMOT (Human and Mouse Orthologous Gene Nomenclature) project is funded by The Wellcome Trust (UK) and supports two staff members, one at HGNC and one at MGI. We aim to approve the equivalent gene symbol for each human/mouse ortholog pair; human gene symbols are written in all uppercase letters, whereas in mouse only the first letter is uppercase and the rest are all lowercase (e.g. human PON2 and mouse Pon2).
The HGNC Comparison of Orthology Predictions search tool, HCOP, enables users to compare orthologs predicted for a specified human gene, or set of human genes. HCOP was originally designed to show orthology predictions between human and mouse in order to identify orthologs with different names. Now with the addition of rat, cow, chicken, C. elegans, dog, fruitfly, chimp, zebrafish and S. cerevisiae there are currently 11 genomes available for comparison in HCOP. We have also recently expanded the number of available orthology resources so that in addition to the Ensembl, HGNC, HomoloGene, Inparanoid and MGI databases we now include Treefam, PhyOP (a dog-human specific dataset), Evola, OMA (Orthologous Matrix project) and UCSC. Previously, researchers had to check in each of these orthology prediction sites in order to determine whether an orthology assertion is agreed by all of these databases. The data returned includes the official nomenclatures, sequences, database identifiers, aliases, and chromosomal locations, for each putative ortholog pair.In the future HCOP could potentially be further expanded, to include orthology information from other orthology prediction databases and for other species.
HCOP will make orthology searching quicker and help to expedite the HUMOT project itself when making orthology assertions between human and mouse genes. Indeed, prior to making HCOP public we have used it to generate comparative files, which are especially useful in identifying human/mouse ortholog pairs with different approved gene symbols. In each case we will attempt to change either the human or mouse approved nomenclature (whenever possible), so that ortholog pairs have the same nomenclature. Potentially this resource can also be expanded to identify predicted orthology assertions between human and other species.
Once all human and mouse orthologous genes have been assigned approved symbols and names, this nomenclature can then proliferate out to other mammalian species as their genomic sequence becomes available. Comparative genomics is an essential constituent of the post-genomic era and the legacy of the HUMOT project will be a standardised nomenclature across species.
HGNC members have attended or will be attending the following meetings to present information on the HUMOT project:
HGM2007 HUGO Human Genome Meeting (Montreal, Canada) 21-24 May 2007
The Biology of Genomes (Cold Spring Harbor, USA) 8-12 May 2007
20th IMGC Annual Meeting (Charleston, South Carolina, USA) 12-15 November 2006
The sixth Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics (Cambridge, UK) 13-17 September 2006
HGM06 HUGO Human Genome Meeting (Helsinki, Finland) 31 May-3 June 2006
19th IMGC Annual Meeting (Strasbourg, France) 5-8 November 2005
Orthologous Transcriptome Nomenclature Meeting (Kyoto, Japan) 22 April 2005
HGM05 HUGO Human Genome Meeting (Kyoto, Japan) 18-21 April 2005
18th IMGC Annual Meeting (Seattle, USA) 18-21 October 2004
The fourth Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics (Cambridge, UK) 22-26 September
Eyre TA, Wright MW, Lush MJ and Bruford EA. HCOP: a searchable database of human orthology predictions. Brief Bioinform. 2006 Sep 2; [Epub ahead of print] PMID:16951416
Wright MW and Bruford EA. Human and orthologous gene nomenclature.Gene. 2006 Mar 15;369:1-6. Epub 2006 Jan 23.PMID:16431039
Wright MW, Eyre TA, Lush MJ, Povey S and Bruford EA. HCOP: The HGNC Comparison of Orthology Predictions Search Tool.Mamm Genome. 2005 Nov; 16(11):827-828. PMID:16284797
|HGNC:||HGNC Comparison of Orthology Predictions Search (HCOP)|
|MGI:||Mammalian Orthology Query|
|MGI's Comparative Maps|
|Human/Mouse Orthology Map|
|Ensembl:||'Orthologue Predictions' in Ensembl gene reports|
|JGI:||Phylogenetically Inferred Groups (PhIGs) Search|
|PhIGs Synteny Viewer|
|Berkeley Lab:||VISTA Genome Browser|
|Wellcome Trust Sanger Institute:||TreeFam|
|H-Invitational Database (H-InvDB):||Evola|
If there are any useful orthology resources that you feel should be included then please let us know.
For further information on the HUMOT project or any human/mouse orthology queries please contact Dr Matt Wright (firstname.lastname@example.org). You can also contact Lois Maltais at MGI (email@example.com).