Skip to contents

Compare Human Pathways with with Other Species

Source: R/reactome_analysis.R
rba_reactome_analysis_species.Rd

Use This function to Compare human's manually-curated pathways and computationally inferred pathways (orthologous) in other species.

Usage

rba_reactome_analysis_species(
  species_dbid,
  sort_by = "ENTITIES_PVALUE",
  order = "ASC",
  resource = "TOTAL",
  p_value = 1,
  min = NULL,
  max = NULL,
  ...
)

Arguments

species_dbid

Numeric: Reactome DbId (e.g Mus musculus is 48892) of the species you want to compare with Homo sapiens. See rba_reactome_species or Reactome Data Schema: Entries: Species.

sort_by

Sort the result based on what column? available choices are: "NAME", "TOTAL_ENTITIES", "TOTAL_INTERACTORS", "TOTAL_REACTIONS", "FOUND_ENTITIES", "FOUND_INTERACTORS", "FOUND_REACTIONS", "ENTITIES_RATIO", "ENTITIES_PVALUE", "ENTITIES_FDR" or "REACTIONS_RATIO"

order

Sort Order. Can be either "ASC" (default) or "DESC".

resource

Filter results based on the resource. Default is "TOTAL", available choices are: "TOTAL", "UNIPROT", "ENSEMBL", "CHEBI", "IUPHAR", "MIRBASE", "NCBI_PROTEIN", "EMBL", "COMPOUND", "ENTITIES_FDR" or "PUBCHEM_COMPOUND".

p_value

Set a P value threshold. Only results with P value equal to or less than your supplied threshold will be returned. (default = 1, Meaning no P value filtering)

min

(numeric) Minimum number of entities that a pathways should have to be included in the results.

max

(numeric) Maximum number of entities that a pathways should have to be included in the results.

...

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

Value

List with the results of the comparison.

Details

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

Corresponding API Resources

"GET https://reactome.org/AnalysisService/species/homoSapiens/{species}"

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 Analysis Services API Documentation

  • Citations note on Reactome website

See also

rba_reactome_orthology

Other "Reactome Analysis Service": rba_reactome_analysis(), rba_reactome_analysis_download(), rba_reactome_analysis_import(), rba_reactome_analysis_mapping(), rba_reactome_analysis_pdf(), rba_reactome_analysis_token()

Examples

# \donttest{
rba_reactome_analysis_species(species_dbid = 48892)
# }