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 or numeric vector of gene identifiers with maximum length of 5,000. Can be any of: Ensembl gene ID, Ensembl protein ID, Ensembl 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

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

References

• Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou L-P, Mi H. (2022) PANTHER: Making genome-scale phylogenetics accessible to all. Protein Science, 31(1), 8–22. https://doi.org/10.1002/pro.4218

• PANTHER Services Details

• Citations note on PANTHER website

See also

Other "PANTHER": rba_panther_enrich(), rba_panther_family(), rba_panther_genome(), 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)
# }