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"
Value
data.table of results from over representation analysis. See PANTHER user manual for column descriptions in "table".
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.
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)
#> number_in_list fold_enrichment fdr expected number_in_reference
#> <int> <num> <num> <num> <int>
#> 1: 14 64.716981 2.713230e-18 0.2163265 106
#> 2: 14 64.716981 2.713230e-18 0.2163265 106
#> 3: 21 17.926829 3.751588e-18 1.1714286 574
#> 4: 21 17.926829 3.751588e-18 1.1714286 574
#> 5: 30 7.080925 1.790665e-17 4.2367347 2076
#> 6: 30 7.080925 1.790665e-17 4.2367347 2076
#> pValue term plus_minus
#> <num> <list> <char>
#> 1: 1.780101e-22 GO:0060070 +
#> 2: 1.780101e-22 canonica.... +
#> 3: 4.922697e-22 GO:0048729 +
#> 4: 4.922697e-22 tissue m.... +
#> 5: 3.524469e-21 GO:0007166 +
#> 6: 3.524469e-21 cell sur.... +