Search PANTHER for Homologs of Gene(s)
Using this function you can search and retrieve homolog of given gene(s).
rba_panther_homolog(genes, organism, type = "P", target_organisms = NA, ...)
genes |
Character vector of genes identifiers with maximum length of 10 or only one if seq_pos is provided. 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 of the organism of your provided
genes. run |
type |
Homolog types to return. either "P" (default) for paralogs, "X" for horizontal gene transfer and "LDX" for diverged horizontal gene transfer. |
target_organisms |
(numeric) NCBI taxon ID(s) to filter the results.
run |
... |
rbioapi option(s). Refer to |
A dataframe with homologs information.
"GET http://www.pantherdb.org/services/oai/pantherdb/ortholog/homologOther"
Mi, H., Muruganujan, A., Ebert, D., Huang, X., & Thomas, P. D. (2019). PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic acids research, 47(D1), D419-D426.
Mi, H., Muruganujan, A., Huang, X., Ebert, D., Mills, C., Guo, X., & Thomas, P. D. (2019). Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v. 14.0). Nature protocols, 14(3), 703-721.
Other "PANTHER":
rba_panther_enrich(),
rba_panther_family(),
rba_panther_info(),
rba_panther_mapping(),
rba_panther_ortholog(),
rba_panther_tree_grafter()
rba_panther_homolog("OR4F5", organism = 9606, type = "P")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.