Forge Tools chea3

chea3 read

scidex.forge.chea3

Predict top driving transcription factors for a gene set using ChEA3 (Chromatin Enrichment Analysis 3, maayanlab.cloud/chea3/). ChEA3 answers the inverse of JASPAR/TFBS queries: given a co-expressed regulon (gene list), which transcription factor most likely drives it? Queries ≥6 background databases (ARCHS4, ENCODE, GTEx, Literature, ReMap, JASPAR) and returns results from integrated mean-rank aggregation. Input: 1–500 HGNC gene symbols, optional limit (default 10). Output: ranked TF predictions with tf_name, rank, score, and overlapping_genes. Same Maayan Lab as Enrichr. API: POST https://maayanlab.cloud/chea3/api/enrich/ — public, no auth.

HTTP: POST /api/scidex/forge/chea3

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.chea3``.",
  "properties": {
    "gene_set": {
      "description": "List of HGNC gene symbols to submit for TF enrichment analysis (e.g. ``['TP53', 'BRCA1', 'MDM2']``). Minimum 1 gene; maximum 500 genes per call.",
      "items": {
        "type": "string"
      },
      "title": "Gene Set",
      "type": "array"
    },
    "background": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional background gene list. Note: the ChEA3 public API uses its own background databases; this parameter is accepted for schema completeness but is not forwarded to the ChEA3 endpoint.",
      "title": "Background"
    },
    "limit": {
      "default": 10,
      "description": "Maximum TF results to return, sorted by rank. Default 10.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_set"
  ],
  "title": "ForgeChEA3In",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "ChEA3Result": {
      "description": "One ranked transcription factor prediction from ChEA3.",
      "properties": {
        "tf_name": {
          "description": "Transcription factor gene symbol (e.g. 'TP53').",
          "title": "Tf Name",
          "type": "string"
        },
        "rank": {
          "description": "Rank in integrated mean-rank output (1 = top predictor).",
          "title": "Rank",
          "type": "integer"
        },
        "score": {
          "description": "Integrated mean-rank score across all ChEA3 libraries (lower = better).",
          "title": "Score",
          "type": "number"
        },
        "overlapping_genes": {
          "description": "Submitted genes overlapping the TF's target gene set.",
          "items": {
            "type": "string"
          },
          "title": "Overlapping Genes",
          "type": "array"
        }
      },
      "required": [
        "tf_name",
        "rank",
        "score"
      ],
      "title": "ChEA3Result",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.chea3``.",
  "properties": {
    "results": {
      "description": "Top-N predicted transcription factors from ChEA3 integrated mean-rank, sorted by rank ascending (rank 1 = strongest predictor).",
      "items": {
        "$ref": "#/$defs/ChEA3Result"
      },
      "title": "Results",
      "type": "array"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream API call (ms).",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "took_ms"
  ],
  "title": "ForgeChEA3Out",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/chea3' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_set": []
}'

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