/ensembl/genes/homologs

POST /api/ensembl/genes/homologs

Price: 20 credits

List the orthologues and paralogues Ensembl Compara records for a gene

How to use it

Comparative genomics rather than a name lookup: it answers what the same gene is called in other species. `homology_type` separates orthologues across species from paralogues within one. A gene Ensembl Compara holds but records no homologue of the requested type answers with an empty list, so an empty list is a biological statement rather than a bad identifier; not found means Compara holds nothing under that id at all - a typo, a gene outside the comparative set, or a `species` that does not match the id's own species. Narrow with `target_species` for one species or `target_taxon` for a clade - unfiltered, a well studied vertebrate gene returns well over a hundred homologues. `homology_type` reports the cardinality (ortholog_one2one, ortholog_one2many), which is what tells a one-to-one match from a family expansion.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• gene string required — Ensembl stable id of the gene whose homologues are wanted (examples: "ENSG00000139618", "ENSG00000012048"; minLength: 1)
• species string — Ensembl species the stable id belongs to (default: "homo_sapiens"; examples: "homo_sapiens"; minLength: 1)
• homology_type string — Which class of homologues to return (default: "all"; one of: "orthologues", "paralogues", "projections", "all")
• target_species string nullable — Keep only homologues in this species (examples: "mus_musculus"; minLength: 1)
• target_taxon integer nullable — Keep only homologues under this NCBI taxon id (examples: 10090, 40674; min: 1)
• alignment_sequence string — Return the aligned sequences of each pair in `align_seq`. They dominate the response, so `none` leaves the alignment to `cigar_line` and the identity percentages (default: "none"; one of: "none", "protein", "cdna")
• count integer required — Max number of homologues to return (min: 1)

Response

• @type string (default: "EnsemblHomology")
• id string required
• gene_id string required
• target_gene_id string (default: "")
• homology_type string (default: "")
• taxonomy_level string (default: "")
• method_link_type string (default: "")
• dn_ds number nullable
• source object nullable
  • @type string (default: "EnsemblHomologyPartner")
  • id string (default: "")
  • protein_id string (default: "")
  • species string (default: "")
  • taxon_id integer nullable
  • identity_percent number nullable
  • positive_percent number nullable
  • cigar_line string (default: "")
  • align_seq string (default: "")
• target object nullable
  • @type string (default: "EnsemblHomologyPartner")
  • id string (default: "")
  • protein_id string (default: "")
  • species string (default: "")
  • taxon_id integer nullable
  • identity_percent number nullable
  • positive_percent number nullable
  • cigar_line string (default: "")
  • align_seq string (default: "")

Errors

• 422 — Unknown species Check the fields against this schema. A URN with the wrong prefix is the most common cause.
• 408 — The request ran past its time limit Raise `timeout` in the request body, up to the maximum this endpoint documents. Lowering `count` or turning off the `with_*` flags also helps, because less work finishes sooner.
• 412 — Gene not found Retrying will not help: either the entity does not exist, or the input points at a different one.
• 429 — Too many requests: a rate limit or a usage window is exhausted When the response carries an X-Retry-After header, wait that many seconds and retry: the same number is in the body as `detail.retry_after`, and the limit clears once that window passes. The message in the body names the limit that was hit.
• 500 — Something broke on our side Retrying will not help. If it keeps happening, send us the X-Request-ID from the response headers.
• 529 — Rate limit reached, or the endpoint is overloaded Wait at least 30 seconds, then retry.

Response headers

• X-Error — Error message text (present only on error)
• X-Request-ID — Unique request identifier
• X-Execution-Time — Execution time in seconds
• X-Result-Count — How many records the body carries. 0 means an empty result, which is a normal answer and not by itself an error. A non-zero count can come back together with X-Error when the failure happened partway through — read this header and X-Error independently.
• X-Total-Available-Results — How many records exist for this query, when the endpoint can say. On a `dry_run` request this is the answer and the body is empty. It saturates: the endpoint's documented maximum means 'at least that many', any smaller number is exact.
• X-Warning — Present when the request body carried keys this endpoint does not document. They were ignored, so any filter you meant to apply through them did not apply. Check the spelling against this schema and retry.
• X-Retry-After — Seconds to wait before retrying. Present only on 429.