rba_reactome_interactors_static {rbioapi} | R Documentation |
Get Static(IntAct) Interaction Information of a Protein
Description
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:
If endpoint = "details" or "summary": Retrieve a detailed/summary information of your supplied protein accession(s) from IntAct database.
If endpoint = "pathway", Retrieve a list of Reactome pathways which include your supplied protein accession. Pathways with the class "TopLevelPathway" will be excluded.
Usage
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:
|
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
|
... |
rbioapi option(s). See |
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
Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028
Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.
See Also
Other "Reactome Content Service - Molecule Interactors":
rba_reactome_interactors_psicquic()
Examples
rba_reactome_interactors_static(proteins = "Q9BXM7-1",
endpoint = "pathways", species = "Homo sapiens")
rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
endpoint = "details")
rba_reactome_interactors_static(proteins = c("Q9BXM7-1", "Q13501"),
endpoint = "summary")