Participating molecules in a Reactome comprises set of 'Physical Entity' and 'Reference Entities' class objects. Use this function to retrieve all, only 'Physical Entity' or only 'Reference Entities' participants of given event.
Usage
rba_reactome_participants(
event_id,
only_physical_entities = FALSE,
only_reference_entities = FALSE,
...
)Arguments
- event_id
Reactome event's database ID (DbId) or Stable ID (StId).
- only_physical_entities
Logical: If TRUe, only participating 'Physical Entities' will be returned.
- only_reference_entities
Logical: If TRUe, only participating 'Reference Entities' will be returned.
- ...
rbioapi option(s). See
rba_options's arguments manual for more information on available options.
Value
List with the participant of your supplied Event ID. A Data frame if only physical or 'Reference Entities' was requested.
Details
A 'Physical Entity' Instance could include an individual molecule,
a multi-molecular complex or a set of molecule forming a group based on
some characteristics. a single molecule can have different 'Physical Entity'
instances based on it's associated attributes. For example, IgK Ig kappa
chain, has two 'Physical Entity' instances; one, with ID
"R-HSA-197041" refers to the secreted antibody protein to the
extra-cellular region; And the second one is with ID
"R-HSA-2038819" and refers to the plasma-membrane-integrated form of
the antibody protein.
To make it possible to link multiple 'Physical Entity' instances of a
molecule, Reactome uses a data class named "'Reference Entities'"
which correspond to the invariant attribute of a molecule. for example,
both of the above-mentioned 'Physical Entities' see a 'Reference Entities'
named
"UniProt:P01834 IGKC.
See Reactome
Data Model for more information about the data model and Physical
Entities.
Corresponding API Resources
"GET https://reactome.org/ContentService/data/participants/{id}"
"GET https://reactome.org/ContentService/data/participants/{id}/
participatingPhysicalEntities"
"GET https://reactome.org/ContentService/data/participants/{id}/
referenceEntities"
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.