Compare Human Pathways with with Other SpeciesSource:
Use This function to Compare human's manually-curated pathways and computationally inferred pathways (orthologous) in other species.
rba_reactome_analysis_species( species_dbid, sort_by = "ENTITIES_PVALUE", order = "ASC", resource = "TOTAL", p_value = 1, min = NULL, max = NULL, ... )
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"
Sort Order. Can be either "ASC" (default) or "DESC".
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".
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)
(numeric) Minimum number of entities that a pathways should have to be included in the results.
(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.
Reactome incorporate manually curated human reactions and PANTHER's
protein homology data to Computationally infer events in other eukaryotic
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.
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.