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

Character: (default = "ENTITIES_PVALUE") 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

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

resource

Character: (default = "TOTAL") Filter results based on the resource. Available choices are: "TOTAL", "UNIPROT", "ENSEMBL", "CHEBI", "IUPHAR", "MIRBASE", "NCBI_PROTEIN", "EMBL", "COMPOUND" or "PUBCHEM_COMPOUND".

p_value

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

min

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

max

Numeric: (optional) 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

A list containing the comparison results. The pathways element is a data frame with information about each pathway expanded into columns; it is an empty data frame when no pathways match.

Details

Reactome incorporate manually curated human reactions and PANTHER's protein homology data to Computationally infer events in other eukaryotic species.
Reactome uses an orthology-based approach to project curated human events to supported non-human species. See Reactome Computationally Inferred Events for more information.

Corresponding API Resources

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

References

  • Ragueneau, E., Gong, C., Sinquin, P., Sevilla, C., Beavers, D., Grentner, A., ... D’Eustachio, P. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Res., 54(D1), D673–D681. doi: 10.1093/nar/gkaf1223

  • Griss, J., Viteri, G., Sidiropoulos, K., Nguyen, V., Fabregat, A., & Hermjakob, H. (2020). ReactomeGSA—Efficient Multi-Omics Comparative Pathway Analysis. Molecular & Cellular Proteomics, 19(12), 2115–2125. doi: 10.1074/mcp.TIR120.002155

  • 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)
# }