Get cross references by gene symbol or name — get_xrefs_by

This function retrieves cross references by symbol or display name of a gene. The data is returned as a tibble where each row is a cross reference related to the provided symbol or display name of a gene. See below under section Value for details about each column.

Usage

get_xrefs_by_gene(
  species_name,
  gene,
  ensembl_db = "core",
  external_db = "",
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Arguments

species_name: The species name, i.e., the scientific name, all letters lowercase and space replaced by underscore. Examples: 'homo_sapiens' (human), 'ovis_aries' (Domestic sheep) or 'capra_hircus' (Goat).
gene: Symbol or display name of a gene, e.g., 'ACTB' or 'BRCA2'.
ensembl_db: Restrict the search to a database other than the default. Ensembl's default database is 'core'.
external_db: Filter by external database, e.g. 'HGNC'. An empty string indicates no filtering.
verbose: Whether to be verbose about the http requests and respective responses' status.
warnings: Whether to show warnings.
progress_bar: Whether to show a progress bar.

Value

A tibble of 12 variables:

species_name: Ensembl species name: this is the name used internally by Ensembl to uniquely identify a species by name. It is the scientific name but formatted without capitalisation and spacing converted with an underscore, e.g., 'homo_sapiens'.
gene: Gene symbol.
ensembl_db: Ensembl database.
primary_id: Primary identification in external database.
display_id: Display identification in external database.
external_db_name: External database name.
external_db_display_name: External database display name.
version: TODO
info_type: There are two types of external cross references (XRef): direct ('DIRECT') or dependent ('DEPENDENT'). A direct cross reference is one that can be directly linked to a gene, transcript or translation object in Ensembl Genomes by synonymy or sequence similarity. A dependent cross reference is one that is transitively linked to the object via the direct cross reference. The value can also be 'UNMAPPED' for unmapped cross references, or 'PROJECTION' for TODO.
info_text: TODO
synonyms: Other names or acronyms used to refer to the gene. Note that this column is of the list type.
description: Brief description of the external database entry.

Ensembl REST API endpoints

get_xrefs_by_gene() makes GET requests to /xrefs/name/:species/:name.

Examples

# Get cross references that relate to gene BRCA2
get_xrefs_by_gene(species_name = 'human', gene = 'BRCA2')
#> # A tibble: 9 × 12
#>   species_name gene  ensembl_db primary_id display_id external_db_name
#>   <chr>        <chr> <chr>      <chr>      <chr>      <chr>           
#> 1 human        BRCA2 core       675        BRCA2      EntrezGene      
#> 2 human        BRCA2 core       1101       BRCA2      GeneCards       
#> 3 human        BRCA2 core       HGNC:1101  BRCA2      HGNC            
#> 4 human        BRCA2 core       A0A7P0TAP7 BRCA2      Uniprot_gn      
#> 5 human        BRCA2 core       A0A8V8TQQ4 BRCA2      Uniprot_gn      
#> 6 human        BRCA2 core       P51587     BRCA2      Uniprot_gn      
#> 7 human        BRCA2 core       A0A7P0T9D7 BRCA2      Uniprot_gn      
#> 8 human        BRCA2 core       675        BRCA2      WikiGene        
#> 9 human        BRCA2 core       IPR015525  BRCA2      Interpro        
#> # ℹ 6 more variables: external_db_display_name <chr>, version <chr>,
#> #   info_type <chr>, info_text <chr>, synonyms <list>, description <chr>