Forge Tools dorothea_regulons

dorothea_regulons read

scidex.forge.dorothea_regulons

Query DoRothEA for transcription factor (TF) regulons — the set of target genes regulated by a given TF, with evidence-graded confidence (A–E). DoRothEA A–B regulons are the gold standard for VIPER/decoupleR TF-activity inference. Data is fetched from OmniPath (omnipathdb.org/interactions?datasets=dorothea). Input: TF gene symbol, min_confidence tier (default B), organism NCBI taxon ID (default 9606 = human), limit. Output: list of TfTarget(target_gene, effect, confidence, evidence_sources), not_found flag. No authentication required. Complements scidex.forge.jaspar_tfbs (binding motifs), scidex.forge.chea3 (inverse enrichment), and scidex.forge.omnipath_interactions (full network).

HTTP: POST /api/scidex/forge/dorothea_regulons

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.dorothea_regulons``.",
  "properties": {
    "tf": {
      "description": "HGNC gene symbol of the transcription factor to query (e.g. ``'TP53'``).",
      "title": "Tf",
      "type": "string"
    },
    "min_confidence": {
      "default": "B",
      "description": "Minimum DoRothEA confidence tier to include. Only targets with confidence ≥ this level (A ≥ B ≥ C ≥ D ≥ E) are returned. Default 'B' balances coverage and reliability.",
      "enum": [
        "A",
        "B",
        "C",
        "D",
        "E"
      ],
      "title": "Min Confidence",
      "type": "string"
    },
    "organism": {
      "default": "9606",
      "description": "NCBI taxonomy ID of the target organism. Default '9606' (Homo sapiens). Other common values: '10090' (Mus musculus), '10116' (Rattus norvegicus).",
      "title": "Organism",
      "type": "string"
    },
    "limit": {
      "default": 50,
      "description": "Maximum number of target records to return (after confidence filter). Default 50.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "tf"
  ],
  "title": "ForgeDorotheaIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "TfTarget": {
      "description": "One DoRothEA TF–target gene interaction record.",
      "properties": {
        "target_gene": {
          "description": "HGNC symbol of the regulated target gene.",
          "title": "Target Gene",
          "type": "string"
        },
        "effect": {
          "description": "Direction of TF regulation: 'stimulation' (activation), 'inhibition' (repression), or 'unknown'.",
          "enum": [
            "stimulation",
            "inhibition",
            "unknown"
          ],
          "title": "Effect",
          "type": "string"
        },
        "confidence": {
          "description": "DoRothEA evidence-convergence tier. A = highest (ChIP+motif+literature+coexpression); E = lowest (inferred).",
          "enum": [
            "A",
            "B",
            "C",
            "D",
            "E"
          ],
          "title": "Confidence",
          "type": "string"
        },
        "evidence_sources": {
          "description": "Evidence databases supporting this TF–target interaction.",
          "items": {
            "type": "string"
          },
          "title": "Evidence Sources",
          "type": "array"
        }
      },
      "required": [
        "target_gene",
        "effect",
        "confidence"
      ],
      "title": "TfTarget",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.dorothea_regulons``.",
  "properties": {
    "tf": {
      "description": "TF gene symbol as queried.",
      "title": "Tf",
      "type": "string"
    },
    "targets": {
      "description": "Target genes regulated by this TF, filtered to min_confidence tier, sorted by confidence (A first) then alphabetically by target_gene. Empty when the TF has no regulon entries in DoRothEA at or above min_confidence.",
      "items": {
        "$ref": "#/$defs/TfTarget"
      },
      "title": "Targets",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when the TF is absent from DoRothEA entirely (the upstream API returned an empty result set for this TF).",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "tf"
  ],
  "title": "ForgeDorotheaOut",
  "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/dorothea_regulons' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "tf": ""
}'

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