Map A Gene-set to PANTHER Database

Using this function, you can search your genes in PANTHER database and retrieve attributes and annotations associated to your genes.

Usage

rba_panther_mapping(genes, organism, ...)

Arguments

genes

Character vector of genes identifiers with maximum length of 1000. Can be any of: Ensemble gene ID, Ensemble protein ID, Ensemble transcript ID, Entrez gene ID, gene symbol, NCBI GI, HGNC ID, International protein index ID, NCBI UniGene ID, UniProt accession and/or UniProt ID.

organism

(numeric) NCBI taxon ID. run rba_panther_info with argument 'what = "organisms"' to get a list of PANTHER's supported organisms.

...

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

Value

A list containing your unmapped inputs and mapped genes with pertinent information.

Corresponding API Resources

"GET https://www.pantherdb.org/services/oai/pantherdb/geneinfo"

References

• Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas, PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D394–D403, https://doi.org/10.1093/nar/gkaa1106

• PANTHER Services Details

• Citations note on PANTHER website

See also

Other "PANTHER": rba_panther_enrich(), rba_panther_family(), rba_panther_homolog(), rba_panther_info(), rba_panther_ortholog(), rba_panther_tree_grafter()

Examples

# \donttest{
rba_panther_mapping(genes = c("Cd40", 7124, "ENSG00000203747", "P33681"),
    organism = 9606)
# }