HCOP Documentation

Overview

The HGNC Comparison of Orthology Predictions (HCOP) search is a tool that integrates and displays the orthology assertions predicted for a specified human gene, or set of human genes, by EnsemblCompara, Evola, HGNC, Homologene, Inparanoid, MGI, OMA, OPTIC, Treefam, UCSC and ZFIN. An indication of the reliability of a prediction is provided by the number of databases which concur and by the presence or absence of synteny between the relevant chromosomes, where known. HCOP was originally designed to show orthology predictions between human and mouse, but now with the addition of chimp, macaque, rat, cow, horse, dog, opossum, platypus, chicken, zebrafish, Drosophila, C. elegans and S. cerevisiae data there are currently 15 genomes available for comparison in HCOP.

Using the search

Orthology assertions can be obtained for a gene by searching with either its approved symbol, Entrez Gene ID, HGNC or MGD ID, or RefSeq ID. The species of the query gene and of the predicted orthologs can optionally be specified. The results provide basic data about the query and its predicted homologs as well as a list of databases that support the assertion and links to further information.

The consensus orthology assertions for multiple genes can be viewed simultaneously by searching with a list of query terms, separated by commas, newlines or spaces.

Searches are case insensitive. The HGNC: or MGI: prefix, and the version number of a RefSeq ID (the last . and following digits) are not required. Only approved nomenclature is shown. Where no name or symbol is given, the relevant nomenclature committee has not yet named this gene.

Synteny

Synteny is assessed on a whole-chromosome basis using the MGI version of the Oxford Grid. A human and a mouse chromosome are stated as syntenic if homology between them would not create a singleton. According to this method the following chromosomes are possibly syntenic:

Origins of the data

The data are stored in a MySQL database for rapid querying. Orthology assertions are stored as pairs of Entrez Gene IDs and an associated list of databases that support that assertion.

Pairs of predicted orthologous Entrez Gene IDs were provided by UCSC and Homologene. Orthologous pairs of Ensembl IDs predicted by Ensembl and Inparanoid were converted to Entrez Gene IDs using data provided by Ensembl. HGNC provide predicted orthologous approved symbols that are converted to Entrez Gene IDs using Ensembl data. Finally, MGI provided predicted pairs of orthologous MGI IDs that were converted to Entrez Gene IDs using MGI mapping data.

The additional data provided by the HGNC Comparison of Orthology Predictions search tool (chromosome, approved symbol and approved name) are derived from the NCBI.

Each of the contributing databases can be accessed via the following links:

Ensembl
Evola (H-InvDB)
HGNC
Homologene
Inparanoid
MGI
OMA
OPTIC
Treefam
UCSC
ZFIN

The HCOP orthology assertions are displayed as tab delimited text from the 'Bulk Downloads' section of the HCOP Search Page on a species by species basis. The '4 Column' output returns the raw assertions and Entrez Gene IDs for human and one other species. The '19 Column' output includes additional information such as the chromosomal location, accession numbers and where possible references the approved gene nomenclature. In addition the full HCOP dataset for all species can be downloaded as a tab delimited text file of either 5 or 20 columns (i.e. the '4 column' or '19 column' options as above but also including an extra column to state the species).

Storing personalised views of the data

Personalised sub-sets of the data can be rapidly accessed by bookmarking the desired results page. Such views can also be directly linked to from other webpages by copying the results page URL. This is particularly useful for comparing the orthology assertions of a set of genes of interest.

Referencing the HGNC Comparison of Orthology Predictions search tool

If you use this tool or the 'Bulk Downloads' in published work please reference:

• 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 PDF
• Eyre TA, Wright MW, Lush MJ and Bruford EA. HCOP: a searchable database of human orthology predictions. Brief Bioinform. 2007 Jan;8(1):2-5. PMID:16951416
• Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA. genenames.org: the HGNC resources in 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D519-9. PMID: 20929869 PDF