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HCOP Search Tool - Beta

HCOP Beta

We are in the process of developing an updated and improved version of HCOP which we hope to release very soon. In addition to the exisiting HCOP species we will also be incoporating data from pig and anole lizard. The version of HCOP displayed here includes the latest datasets from the following orthology resources:

  • Homologene
  • Inparanoid*
  • Ensembl Compara
  • Panther
  • OrthoDB
  • OMA
  • Treefam
  • HGNC
  • ZFIN

Currently we are displaying data for human orthologs to chimp, mouse and rat only, remaining species will be added shortly. In addition to the new datasets the HCOP tool interface will be changing to make it more user friendly. Changes to the interface will be made incrementally on this beta page to allow users to test the changes and provide us with any feedback as to what they do and don't like. If you have any requests either for ortholog datasets you would like us to include or for HCOP features you would like to see please let us know by emailing hgnc@genenames.org. Please note this is a work in progress so some functionality that exists in the original HCOP may not yet have been added and some features may not work perfectly.

* Inparanoid data for chimp is excluded due to a problem with the source data.

HCOP:HGNC Comparison of Orthology Predictions

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Search tips:

  • 'Return data as text' returns the results as a tab delimited text file. The layout of this table is subject to change as a result of user feedback and new fields being added to HCOP.
  • The 'Reciprocal Search' option displayed in the results for each orthology prediction search enables users to run the reverse species-to-species search. The search uses the NCBI Entrez Gene ID for the returned ortholog, i.e. a human to mouse search with ABCA1 hits mouse Gene ID 11303, so the reciprocal search would be for mouse to human with Gene ID 11303. Sometimes a one-to-one relation between human and mouse is a one-to-many relation from mouse to human
  • HCOP supports wild cards. Use _ to substitue for a single character and * or % to substitue for ) or more characters. For example ABCA* fetches all ABCA genes, ABCA_ fetches ABCA1 to ABCA9. It is not advisable to start a query with a wildcard as the database will not be able to use its indexes and the search will be slow.
  • If provided with a list of terms (either comma, space or newline delimited), HCOP searches with each term in turn e.g. ABCA1 ABCA2 ABCA3. A file containing the list can be uploaded using the "upload a file" search.
  • HCOP supports searching approved gene names. Select the 'Approved Gene name that contains' option and enter the search string (this option takes longer than symbol or ID based searches). This option supports wild cards, thus a search for ATP*cardiac would bring up all names containing ATP followed at some point by cardiac (i.e. ATPAse, Ca++ transporting, cardiac muscle, fast twitch 1 and ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle, etc).
    • Note: Since approved names can contain commas and spaces this option only accepts newline delimited lists, i.e. a list of names one per line. This list can be copy/pasted to the search form or uploaded as a file.

Notes:

(1) There is currently no Horse, Cow, Chimp, Macaque, Opossum, Platypus. or Dog Gene Nomenclature Committee. These symbols and names are derived from NCBI data