Forge Tools gtrd_tfbs

gtrd_tfbs read

scidex.forge.gtrd_tfbs

Query GTRD (Gene Transcription Regulation Database, gtrd.biouml.org) for experimental transcription factor binding sites from ChIP-seq experiments. GTRD integrates 50,000+ human ChIP-seq experiments covering 674 human TFs and provides consensus merged binding peaks with experiment-count confidence. Distinct from JASPAR (motif predictions) and ChEA3 (enrichment analysis): GTRD gives actual genomic coordinates of experimentally validated binding sites. Two query modes: 'target_gene' (find all TFs binding near a gene's promoter) and 'tf' (find all binding sites for a given TF). Optional TF filter for target_gene queries. Input: gene, query_type (default 'target_gene'), tf (optional filter), genome (default 'hg38'), limit. Output: binding_sites with tf_name, chrom, start, end, peak_count, confidence; not_found flag. Free API, no auth required. API: https://gtrd.biouml.org/biouml/rest/

HTTP: POST /api/scidex/forge/gtrd_tfbs

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.gtrd_tfbs``.",
  "properties": {
    "gene": {
      "description": "HGNC gene symbol to query. When ``query_type='target_gene'``, finds TF binding sites near this gene's promoter/body (e.g. 'MYC', 'TP53'). When ``query_type='tf'``, used as a secondary filter; set ``tf`` to specify the transcription factor instead.",
      "title": "Gene",
      "type": "string"
    },
    "query_type": {
      "default": "target_gene",
      "description": "Query mode. ``'target_gene'`` (default): find all TFs with ChIP-seq binding sites near the given gene. ``'tf'``: find all binding sites for the TF named in ``gene`` (or filtered by ``tf``).",
      "title": "Query Type",
      "type": "string"
    },
    "tf": {
      "default": "",
      "description": "Optional TF symbol filter (e.g. 'CTCF'). When set and ``query_type='target_gene'``, restricts results to sites from this TF. When ``query_type='tf'``, specifies which TF to query (overrides ``gene``).",
      "title": "Tf",
      "type": "string"
    },
    "genome": {
      "default": "hg38",
      "description": "Reference genome assembly. Default ``'hg38'``. Also accepts ``'hg19'``, ``'mm10'``, ``'mm39'`` for other species.",
      "title": "Genome",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of binding site records to return. Default 20.",
      "maximum": 500,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgeGtrdTfbsIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "GtrdSite": {
      "description": "One GTRD merged ChIP-seq binding site record.",
      "properties": {
        "tf_name": {
          "description": "HGNC symbol of the transcription factor (e.g. 'MYC').",
          "title": "Tf Name",
          "type": "string"
        },
        "chrom": {
          "description": "Chromosome (e.g. 'chr8').",
          "title": "Chrom",
          "type": "string"
        },
        "start": {
          "description": "0-based genomic start coordinate.",
          "title": "Start",
          "type": "integer"
        },
        "end": {
          "description": "Genomic end coordinate (exclusive).",
          "title": "End",
          "type": "integer"
        },
        "peak_count": {
          "description": "Number of ChIP-seq experiment peaks merged into this consensus site. Higher values indicate broader experimental support.",
          "minimum": 1,
          "title": "Peak Count",
          "type": "integer"
        },
        "confidence": {
          "description": "Qvalue / confidence score for the merged peak (lower = more significant). Set to 0.0 when not reported by the API.",
          "title": "Confidence",
          "type": "number"
        }
      },
      "required": [
        "tf_name",
        "chrom",
        "start",
        "end",
        "peak_count",
        "confidence"
      ],
      "title": "GtrdSite",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.gtrd_tfbs``.",
  "properties": {
    "gene": {
      "description": "The gene symbol that was queried.",
      "title": "Gene",
      "type": "string"
    },
    "query_type": {
      "description": "The query mode used ('target_gene' or 'tf').",
      "title": "Query Type",
      "type": "string"
    },
    "binding_sites": {
      "description": "GTRD merged ChIP-seq binding sites matching the query, capped at ``limit``. Sorted by peak_count descending (highest experimental support first).",
      "items": {
        "$ref": "#/$defs/GtrdSite"
      },
      "title": "Binding Sites",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no binding sites were found for the given query.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "gene",
    "query_type"
  ],
  "title": "ForgeGtrdTfbsOut",
  "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/gtrd_tfbs' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene": ""
}'

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