rba_reactome_orthology: Get Orthologous (Computationally Inferred) Events

In rbioapi: User-Friendly R Interface to Biologic Web Services' API

Get Orthologous (Computationally Inferred) Events

Description

Reactome incorporate manually curated human reactions and PANTHER's protein homology data to Computationally infer events in other eukaryotic species.

Usage

rba_reactome_orthology(event_ids, species_dbid, ...)

Arguments

event_ids	Human Reactome event ID(s) to retrieve their orthologous events.
species_dbid	Reactome database ID (DbId) of the target species. (e.g Mus musculus is 48892). 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.

Details

In version 73 (11 June 2020), using an orthology-based approach, Homo sapiens events was projected to 18,654 orthologous pathways (with 81,835 orthologous proteins) in 15 non-human species.
See Reactome Computationally Inferred Events for more information.

Value

List containing found Orthologous event(s) in your supplied species and their pertinent information.

Corresponding API Resources

"POST https://reactome.org/ContentService/data/orthologies/ids/ species/{speciesId}"

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.

• Reactome Content Services API Documentation

• Citations note on Reactome website

See Also

rba_reactome_analysis_species

Examples

rba_reactome_orthology(event_ids = c("R-HSA-6799198", " R-HSA-72764"),
    species_dbid = 49633)

rbioapi documentation built on April 4, 2025, 5:04 a.m.