HCOP: The HGNC comparison of orthology predictions search tool
Mathew W. Wright, Tina A. Eyre, Michael J. Lush, Sue Povey, Elspeth A. Bruford
HUGO Gene Nomenclature Committee, The Galton Laboratory, Department of Biology, University College London, Wolfson House, 4,
Stephenson Way, London, NW1 2HE, UK
Received: 28 July 2005 / Accepted: 4 October 2005
The HGNC Comparison of Orthology Predictions
search tool, HCOP (http://www.gene.ucl.ac.uk/cgi-
bin/nomenclature/hcop.pl), enables users to com-
pare predicted human and mouse orthologs for a
specified gene, or set of genes, from either species
according to the ortholog assertions from the En-
sembl, HGNC, Homologene, Inparanoid, MGI and
PhIGs databases. Users can assess the reliability of
the prediction from the number of these different
sources that identify a particular orthologous pair.
HCOP provides a useful one-stop resource to sum-
marise, compare and access various sources of hu-
man and mouse orthology data.
Orthologs are genes in different species that
derive from a common ancestor without duplica-
tion, and generally share the same function. The
HUGO Gene Nomenclature Committee (HGNC)
collaborates with the Mouse Genomic Nomencla-
ture Committee in order to reduce interspecies
nomenclature confusion by assigning, where pos-
sible, the equivalent gene symbol to orthologous
human and mouse genes (e.g., PON2 in human,
Pon2 in mouse).
Establishing orthology relationships is a major
task in the post-genomic era. Various groups report
orthology information but a single tool for compar-
ison of these data to identify a consensus of the or-
thology predictions has not previously been
available. The new HGNC Comparison of Orthology
Predictions search tool, HCOP, found at http://
fulfills this role for human and mouse genes. It re-
turns orthology assertions made by Ensembl
(Hubbard et al. 2005), HGNC (Wain et al. 2004),
Homologene (Wheeler et al. 2005), Inparanoid
(Remm et al. 2001; O’’Brien et al. 2005), MGI (Eppig
et al. 2005) and PhIGs (Dehal & Boore 2005).
Documentation and help is available at http://www.
A comparison of orthology assertions for a hu-
man or mouse gene can be obtained by searching
HCOP with either an approved symbol (e.g., PON2),
a term from an approved gene name (e.g., ‘‘oxon-
ase’’), Entrez Gene ID, HGNC ID or MGI ID, or
RefSeq accession (e.g., NM_000305; Pruitt et al.
2005). A file containing a list of identifiers can also
be uploaded to facilitate multiple searches. The re-
sults return the official nomenclatures, sequence
accessions, database identifiers, aliases, and chro-
mosomal locations for each putative ortholog pair.
As conservation of synteny occurs throughout
mammalian genomes and is a reliable indicator of
orthology, HCOP also indicates whether the human
and mouse ortholog are from syntenic chromo-
somes. A list of databases that support each assertion
and links to sources of further information about
these databases are also provided.
Paralogs are genes within a specific genome re-
lated by duplication from a common ancestor. En-
sembl, Inparanoid and Homologene sometimes
return more than one predicted ortholog, which
usually indicates the presence of closely related
paralogs. Inparanoid also differentiates between
inparalogs and outparalogs; inparalogs arise through
a gene duplication event after speciation, whereas
outparalogs arise following a gene duplication before
speciation (Remm et al. 2001; O’’Brien et al. 2005).
Hence, where an HCOP search shows more than one
predicted ortholog for any gene in one species, this
may be indicative of paralogy as reported by the
Correspondence to: Mathew W. Wright; E-mail: nome@galton.
DOI: 10.1007/s00335-005-0103-2 Volume 16, 827À828 (2005) Ó Springer Science+Business Media, Inc. 2005