Forge Tools fantom5_enhancers

fantom5_enhancers read

scidex.forge.fantom5_enhancers

Query the FANTOM5 database (fantom.gsc.riken.jp/5/) for cell type-specific enhancer activity profiles. FANTOM5 identified 43,011 permissive enhancers using CAGE-seq across 1,829 human cell types and primary tissues (Andersson et al., Nature 2014). Returns enhancers with chromosomal coordinates, putative target genes, active cell types, and max CAGE signal (TPM). Supports gene-based lookup (enhancers targeting a gene) and cell type filtering. Critical gap vs. ENCODE: provides CAGE-based enhancer activity profiles that ENCODE epigenomics and Ensembl regulatory verbs do not supply. Free public data, no authentication required.

HTTP: POST /api/scidex/forge/fantom5_enhancers

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.fantom5_enhancers``.",
  "properties": {
    "gene": {
      "default": "",
      "description": "HGNC gene symbol to find putative enhancers targeting this gene (e.g. 'MYC', 'TP53'). Returns enhancers with significant CAGE–gene correlation. Supply at least one of ``gene`` or ``cell_type``.",
      "title": "Gene",
      "type": "string"
    },
    "cell_type": {
      "default": "",
      "description": "Cell type or tissue name filter (e.g. 'hepatocyte', 'CD4-positive T cell'). Partial, case-insensitive match against FANTOM5 cell type names. Supply at least one of ``gene`` or ``cell_type``.",
      "title": "Cell Type",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of enhancer records to return. Default 20.",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeFantom5EnhancersIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "Enhancer": {
      "description": "One FANTOM5 permissive enhancer record.",
      "properties": {
        "enhancer_id": {
          "description": "Genomic coordinate ID (e.g. 'chr8:127735434-127736047').",
          "title": "Enhancer Id",
          "type": "string"
        },
        "chr": {
          "description": "Chromosome (e.g. 'chr8').",
          "title": "Chr",
          "type": "string"
        },
        "start": {
          "description": "0-based start coordinate (BED format).",
          "title": "Start",
          "type": "integer"
        },
        "end": {
          "description": "End coordinate (exclusive, BED format).",
          "title": "End",
          "type": "integer"
        },
        "target_gene": {
          "description": "HGNC symbol of the putative target gene correlated with this enhancer.",
          "title": "Target Gene",
          "type": "string"
        },
        "cell_types": {
          "description": "Cell types or tissues where this enhancer is active (CAGE expression > 0).",
          "items": {
            "type": "string"
          },
          "title": "Cell Types",
          "type": "array"
        },
        "max_tpm": {
          "description": "Maximum CAGE signal (TPM) observed across all cell types for this enhancer.",
          "minimum": 0,
          "title": "Max Tpm",
          "type": "number"
        },
        "permissive": {
          "default": true,
          "description": "True for permissive FANTOM5 enhancers (Andersson 2014 set); False for robust (more stringent) subset.",
          "title": "Permissive",
          "type": "boolean"
        }
      },
      "required": [
        "enhancer_id",
        "chr",
        "start",
        "end",
        "target_gene",
        "max_tpm"
      ],
      "title": "Enhancer",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.fantom5_enhancers``.",
  "properties": {
    "query": {
      "description": "The gene symbol or cell type that was queried (primary search term).",
      "title": "Query",
      "type": "string"
    },
    "enhancers": {
      "description": "FANTOM5 permissive enhancers matching the query, capped at ``limit``. Sorted by max_tpm descending (most active enhancers first).",
      "items": {
        "$ref": "#/$defs/Enhancer"
      },
      "title": "Enhancers",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no FANTOM5 enhancers were found for the given gene or cell type.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeFantom5EnhancersOut",
  "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/fantom5_enhancers' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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