Gtex Tools#

Configuration File: gtex_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the gtex_tools.json configuration file.

Available Tools#

GTEx_get_expression_summary (Type: GTExExpressionTool)#

Summarize tissue-specific expression (e.g., median TPM) for a gene across GTEx tissues. Accepts g…

GTEx_get_expression_summary tool specification

Tool Information:

  • Name: GTEx_get_expression_summary

  • Type: GTExExpressionTool

  • Description: Summarize tissue-specific expression (e.g., median TPM) for a gene across GTEx tissues. Accepts gene symbols (TP53, BRCA1) or Ensembl IDs and verifies their mapping to the dataset-compatible versioned GENCODE ID before querying expression. An unknown gene or resolver failure returns an error rather than an empty successful expression profile. Use to profile baseline expression patterns for targets/biomarkers.

Parameters:

  • gene_symbol (string) (optional) Gene symbol (e.g., ‘TP53’, ‘BRCA1’, ‘FBN1’). Auto-resolved to versioned GENCODE ID.

  • ensembl_gene_id (string) (optional) Ensembl gene identifier (e.g., ‘ENSG00000141510’ or ‘ENSG00000141510.11’). Use gene_symbol instead if you have a gene name.

Example Usage:

query = {
    "name": "GTEx_get_expression_summary",
    "arguments": {
    }
}
result = tu.run(query)

GTEx_query_eqtl (Type: GTExEQTLTool)#

Query GTEx single-tissue eQTL associations for a gene. Accepts gene symbols (TP53, BRCA1) or Ense…

GTEx_query_eqtl tool specification

Tool Information:

  • Name: GTEx_query_eqtl

  • Type: GTExEQTLTool

  • Description: Query GTEx single-tissue eQTL associations for a gene. Accepts gene symbols (TP53, BRCA1) or Ensembl IDs and verifies their mapping to the dataset-compatible versioned GENCODE ID before querying associations. An unknown gene or resolver failure returns an error rather than an empty successful eQTL result. Use to identify regulatory variants (variantId, pValue, slope) relevant to expression regulation.

Parameters:

  • gene_symbol (string) (optional) Gene symbol (e.g., ‘TP53’, ‘BRCA1’). Auto-resolved to versioned GENCODE ID.

  • ensembl_gene_id (string) (optional) Ensembl gene identifier (e.g., ‘ENSG00000141510’). Use gene_symbol instead if you have a gene name.

  • gene_id (string) (optional) Alias for ensembl_gene_id. Ensembl gene ID (e.g., ‘ENSG00000141510’).

  • gene_input (string) (optional) Alias for gene_symbol. Gene symbol or Ensembl ID (e.g., ‘TP53’, ‘ENSG00000141510’).

  • tissue_id (string) (optional) GTEx tissue ID to filter eQTL results (e.g., ‘Brain_Cortex’, ‘Whole_Blood’, ‘Liver’). Case-sensitive.

  • tissue (string) (optional) Alias for tissue_id. GTEx tissue name (e.g., ‘Brain_Cortex’, ‘Whole_Blood’).

  • page (integer) (optional) Page number (1-based).

  • size (integer) (optional) Number of records per page (1–100).

Example Usage:

query = {
    "name": "GTEx_query_eqtl",
    "arguments": {
    }
}
result = tu.run(query)