functional_enrichment
ActiveTool of com.seqbench/workbench
declared in 1.1.0
Over-representation analysis: test which GO terms (biological process / molecular function / cellular component) and Reactome pathways are statistically enriched in a query gene list versus a background, using the hypergeometric test with Benjamini-Hochberg FDR correction across all tested terms. Uses bundled GO Consortium + Reactome reference data (human only). KEGG is not included (its license does not permit bundling gene sets).
Parameters schema
{
"type": "object",
"required": [
"genes"
],
"properties": {
"genes": {
"type": "array",
"items": {
"type": "string"
},
"description": "Query gene symbols (human, e.g. \"TP53\"). Case-insensitive. Capped at 5000."
},
"background": {
"type": "array",
"items": {
"type": "string"
},
"description": "Custom background/universe gene symbols. If omitted, defaults to every gene present in the bundled GO+Reactome dataset (the 'only annotated genes' convention, as used by g:Profiler) rather than the whole genome."
},
"collections": {
"type": "array",
"items": {
"enum": [
"GO:BP",
"GO:MF",
"GO:CC",
"Reactome"
],
"type": "string"
},
"default": [
"GO:BP",
"GO:MF",
"GO:CC",
"Reactome"
],
"description": "Which term collections to test. Defaults to all four."
},
"maxTermSize": {
"type": "integer",
"default": 500,
"description": "Skip terms/pathways with more than this many background genes (matches clusterProfiler's default)."
},
"minTermSize": {
"type": "integer",
"default": 3,
"description": "Skip terms/pathways with fewer than this many background genes."
}
},
"additionalProperties": false
}Parent server
com.seqbench/workbench
1/7 registries