Search PANTHER for Homologs of Gene(s)

Using this function you can search and retrieve homolog of given gene(s).

Usage

rba_panther_homolog(genes, organism, type = "P", target_organisms = NULL, ...)

Arguments

genes

Character or numeric vector of gene identifiers with maximum length of 10. 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 of the organism of your supplied genes. run rba_panther_info with argument 'what = "organisms"' to get a list of PANTHER's supported organisms.

type

Homolog types to return. either "P" (default) for paralogs, "X" for horizontal gene transfer and "LDX" for least diverged horizontal gene transfer.

target_organisms

(numeric) NCBI taxon ID(s) to filter the results. run rba_panther_info with argument 'what = "organisms"' to get a list of PANTHER's supported organisms. This argument is ignored for paralogs, which are searched within the input organism. For horizontal gene transfers, target organisms should differ from the input organism.

...

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

Value

A data frame with homolog information.

Corresponding API Resources

"POST https://www.pantherdb.org/services/oai/pantherdb/ortholog/homologOther"

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_info(), rba_panther_mapping(), rba_panther_ortholog(), rba_panther_tree_grafter()

Examples

# \donttest{
rba_panther_homolog("OR4F5", organism = 9606, type = "P")
# }