Reactome maintain a locally host a version of IntAct(Static) interactions database. Using this function, you can retrieve IntAct information of a protein(s) in two scenarios:

  1. If endpoint = "details" or "summary": Retrieve a detailed/summary information of your supplied protein accession(s) from IntAct database.

  2. If endpoint = "pathway", Retrieve a list of Reactome pathways which include your supplied protein accession. Pathways with the class "TopLevelPathway" will be excluded.

rba_reactome_interactors_static(
  proteins,
  endpoint = "details",
  only_diagrammed = FALSE,
  species = NULL,
  ...
)

Arguments

proteins

Uniprot proteins accession(s). If endpoint = "pathway", only a single protein accession can be supplied.

endpoint

Can be one of:

  1. "details": To return a detailed information of your supplied protein(s) accession.

  2. "summary": To return a summary of your supplied protein(s) accession

  3. "pathway": To return a list of pathways containing the interacting molecules (excluding TopLevelPathway class).

only_diagrammed

Logical: (only when "endpoint = "pathway") If TRUE, pathways without diagram will be excluded. (default = FALSE)

species

Only when "endpoint = "pathway", The scientific name of the species to search for the pathways. See rba_reactome_species or Reactome Data Schema: Entries: Species.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

List which it's content varies based on the supplied "endpoint" argument.

Corresponding API Resources

"POST https://reactome.org/ContentService/interactors/static/ molecules/details"
"POST https://reactome.org/ContentService/interactors/static/ molecules/summary"
"GET https://reactome.org/ContentService/interactors/static/ molecules/pathways"

References

  • Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031. PubMed PMID: 31691815.

  • Reactome Content Services API Documentation

See also

Other "Reactome Content Service - Molecule Interactors": rba_reactome_interactors_psicquic()

Examples

# \donttest{
rba_reactome_interactors_static(proteins = "Q9BXM7-1",
    endpoint = "pathways", species = "Homo sapiens")
# }
# \donttest{
rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
    endpoint = "details")
# }
# \donttest{
rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
    endpoint = "summary")
# }