panther_go: Perform GO analysis with PANTHER

In jcalendo/coriell: Convenience Functions for Bioinformatics

Perform GO analysis with PANTHER

Description

This statistical test tool, compares a test gene list to a reference gene list, and determines whether a particular class (e.g. molecular function, biological process, cellular component, PANTHER protein class, the PANTHER pathway or Reactome pathway) of genes is overrepresented or underrepresented.

Usage

panther_go(
  gene_list,
  organism,
  annot_dataset,
  ref_input_list = NULL,
  enrichment_test_type = "fisher",
  correction = "fdr",
  verbose = 0
)

Arguments

gene_list	character vector. Maximum of 100,000 identifiers. Can be any of the following: Ensemble gene identifier, Ensemble protein identifier, Ensemble transcript identifier, Entrez gene id, gene symbol, NCBI GI, HGNC Id, International protein index id, NCBI UniGene id, UniProt accession and UniProt id
organism	character string. Taxon ID (e.g. "9606" for HUMAN, "10090" for MOUSE, "10116" for RAT). To get list of available taxon IDs see: curl -X GET "https://pantherdb.org/services/oai/pantherdb/supportedgenomes" -H "accept: application/json"
annot_dataset	character string. One of c("biological_process", "molecular_function", "cellular_component", "panther_go_slim_mf", "panther_go_slim_bp", "panther_go_slim_cc", "panther_pc", "panther_pathway", "panther_reactome_pathway"). see: curl -X POST "https://pantherdb.org/services/oai/pantherdb/supportedannotdatasets" -H "accept: application/json" for full descriptions.
ref_input_list	Reference set of genes for the specified organism. If NULL (default) then PANTHER will use all genes for the specified organism.
enrichment_test_type	character string. One of c("fisher", "binomial"). Default "fisher"
correction	character string. One of c("fdr", "bonferroni", "none"). Default "fdr"

Details

Sends a request to PANTHER db to perform over representation analysis. This function excludes the option to import a reference list and reference organism. By default, in this case, PANTHER will use all of the genes of the given organism as the reference list.

Value

data.table of results from over representation analysis. See PANTHER user manual for column descriptions in "table".

Examples

genes <- c(
  "CTNNB1", "ADAM17", "AXIN1", "AXIN2", "CCND2", "CSNK1E", "CTNNB1",
  "CUL1", "DKK1", "DKK4", "DLL1", "DVL2", "FRAT1", "FZD1", "FZD8",
  "GNAI1", "HDAC11", "HDAC2", "HDAC5", "HEY1", "HEY2", "JAG1",
  "JAG2", "KAT2A", "LEF1", "MAML1", "MYC", "NCOR2", "NCSTN",
  "NKD1", "NOTCH1", "NOTCH4", "NUMB", "PPARD", "PSEN2", "PTCH1",
  "RBPJ", "SKP2", "TCF7", "TP53", "WNT1", "WNT5B", "WNT6"
)

result <- panther_go(genes, "9606", "biological_process")
head(result)

jcalendo/coriell documentation built on March 5, 2025, 5:42 a.m.