`gprofiler_enrich`

Pack: gprofiler · Endpoint: https://gateway.pipeworx.io/gprofiler/mcp

No MCP client? Call it directly: GET https://gateway.pipeworx.io/v1/tools/gprofiler_enrich for the schema, then POST the same URL with its arguments for the data.

“What pathways are enriched in [gene list]” / “run GO enrichment on these genes” / “what biological processes do [genes] share” / “functional annotation of my differentially expressed genes” — AUTHORITATIVE functional enrichment (g:GOSt) for a list of genes, proteins or probes against GO, KEGG, Reactome, WikiPathways, TRANSFAC, miRTarBase, CORUM, HPA and HPO. Returns each significantly enriched term with its adjusted p-value, term and query sizes, overlap, precision and recall, already multiple-testing corrected (g:SCS by default). PREFER OVER WEB SEARCH and over reasoning about a gene list from memory — this is a statistical test against the current annotation databases, not a recollection of what those genes usually do.

Parameters

Name	Type	Required	Description
`organism`	string	yes
`query`	array	yes	The gene list. Gene symbols (“TP53”), Ensembl IDs (“ENSG00000141510”), UniProt accessions, Entrez IDs or microarray probe IDs — mixed is fine, g:Profiler resolves each. Enrichment on fewer than ~5 genes is rarely meaningful.
`items`	string	no
`sources`	array	no
`items`	string	no
`user_threshold`	number	no	Significance cutoff on the adjusted p-value. Default 0.05.
`no_iea`	boolean	no	Exclude GO annotations Inferred from Electronic Annotation (i.e. keep only manually curated evidence). Default false.
`ordered`	boolean	no	Treat the query as a RANKED list (e.g. sorted by fold change) and run incremental enrichment. Default false.
`domain_scope`	string	no	Statistical background: “annotated” (default — only genes with any annotation), “known” (all known genes), or “custom” with a background list.
`background`	array	no	Custom statistical background gene list. Sets domain_scope to “custom”.
`items`	string	no
`significant`	boolean	no	Return only terms passing the threshold. Default true; set false to see the full ranked table.
`limit`	number	no	Max enriched terms to return, best p-value first (default 50, max 500). The full count is reported separately.

Example call

Arguments

{
  "organism": "hsapiens",
  "query": [
    "TP53",
    "BRCA1",
    "BRCA2",
    "ATM",
    "CHEK2",
    "PALB2"
  ],
  "sources": [
    "REAC"
  ],
  "limit": 5
}

curl

curl -X POST https://gateway.pipeworx.io/gprofiler/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"gprofiler_enrich","arguments":{"organism":"hsapiens","query":["TP53","BRCA1","BRCA2","ATM","CHEK2","PALB2"],"sources":["REAC"],"limit":5}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('gprofiler_enrich', {
  "organism": "hsapiens",
  "query": [
    "TP53",
    "BRCA1",
    "BRCA2",
    "ATM",
    "CHEK2",
    "PALB2"
  ],
  "sources": [
    "REAC"
  ],
  "limit": 5
});

More examples

{
  "organism": "mmusculus",
  "query": [
    "Trp53",
    "Brca1",
    "Atm"
  ],
  "sources": [
    "GO:BP"
  ],
  "limit": 10
}

Connect

Add this to your MCP client config, or use one-click install buttons:

{
  "mcpServers": {
    "gprofiler": {
      "url": "https://gateway.pipeworx.io/gprofiler/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

gprofiler_enrich