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HGNC Comparison of Orthology Predictions | |
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| Giving unique and meaningful names to every human gene | ||||||||
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 Ensembl, Evola, HGNC, Homologene, Inparanoid, MGI, OMA, PhIGS, PhyOP, Treefam and ZFIN. An indication of the reliabilty 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 rat, chicken, dog, fruitfly, chimp and zebrafish data there are currently 8 genomes available for comparison in HCOP.
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 simulaneously 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 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 syntenic:
| Human Chromosome | Syntenic Mouse Chromosomes | Human Chromosome | Syntenic Mouse Chromosomes |
|---|---|---|---|
| 1 | 1 3 4 5 8 11 | 2 | 1 2 5 6 10 11 12 17 18 |
| 3 | 3 6 9 14 16 17 | 4 | 3 5 6 8 |
| 5 | 1 11 13 15 17 18 | 6 | 1 4 9 10 13 17 |
| 7 | 5 6 9 11 12 13 | 8 | 1 3 4 8 14 15 |
| 9 | 2 4 13 19 | 10 | 2 6 7 8 10 13 14 18 19 |
| 11 | 2 7 9 19 | 12 | 5 6 10 15 |
| 13 | 1 3 5 8 14 | 14 | 12 14 |
| 15 | 2 7 9 | 16 | 7 8 16 17 |
| 17 | 11 | 18 | 1 17 18 |
| 19 | 7 8 9 10 17 | 20 | 2 |
| 21 | 10 16 17 | 22 | 5 6 8 10 11 15 16 |
| X | X | Y | Y |
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 Homologene. Orthologous pairs of Ensembl IDs predicted by Ensembl, Inparanoid and PhIGs 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 URLs:
Ensembl http://www.ensembl.org
Evola (H-InvDB)
http://h-invitational.jp/hinv/EVOLa/
HGNC http://www.genenames.org/
Homologene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=homologene
Inparanoid http://inparanoid.sbc.su.se/
MGI http://www.informatics.jax.org/
OMA http://omabrowser.org/
PhIGs http://phigs.jgi-psf.org
Treefam http://www.treefam.org
ZFIN http://zfin.org
The HCOP Human/Mouse orthology assertions are available as a tab delimited text file here.
There is also a 'lite' version of this file which only contains the orthology assertions and the Entrez Gene IDs here.
If you use this tool or the associated data in published work please reference:
NHGRI |
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