Expression Atlas ToolsĀ¶

Configuration File: expression_atlas_tools.json Tool Type: Local Tools Count: 4

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

Available ToolsĀ¶

ExpressionAtlas_get_baseline (Type: ExpressionAtlasTool)Ā¶

Get baseline gene expression experiments from EBI Expression Atlas. Shows which tissues/cell typeā€¦

ExpressionAtlas_get_baseline tool specification

Tool Information:

  • Name: ExpressionAtlas_get_baseline

  • Type: ExpressionAtlasTool

  • Description: Get baseline gene expression experiments from EBI Expression Atlas. Shows which tissues/cell types express a gene under normal conditions. Complements GTEx and HPA. No API key needed. Query by gene symbol or Ensembl ID.

Parameters:

  • gene (string) (required) Gene symbol (e.g., ā€˜TP53ā€™, ā€˜WDR7ā€™) or Ensembl ID (e.g., ā€˜ENSG00000141510ā€™)

  • species (string) (optional) Species name (default: ā€˜homo sapiensā€™). Also supports ā€˜mus musculusā€™, ā€˜rattus norvegicusā€™, etc.

Example Usage:

query = {
    "name": "ExpressionAtlas_get_baseline",
    "arguments": {
        "gene": "example_value"
    }
}
result = tu.run(query)

ExpressionAtlas_get_experiment (Type: ExpressionAtlasTool)Ā¶

Get detailed metadata for a specific Expression Atlas experiment by accession (e.g., E-MTAB-5214)ā€¦

ExpressionAtlas_get_experiment tool specification

Tool Information:

  • Name: ExpressionAtlas_get_experiment

  • Type: ExpressionAtlasTool

  • Description: Get detailed metadata for a specific Expression Atlas experiment by accession (e.g., E-MTAB-5214). Returns experiment design, species, technology, contrasts, PubMed references, and number of assays.

Parameters:

  • accession (string) (required) Expression Atlas experiment accession (e.g., ā€˜E-MTAB-5214ā€™, ā€˜E-GEOD-26284ā€™)

Example Usage:

query = {
    "name": "ExpressionAtlas_get_experiment",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

ExpressionAtlas_search_differential (Type: ExpressionAtlasTool)Ā¶

Search for differential expression experiments from EBI Expression Atlas. Find experiments where ā€¦

ExpressionAtlas_search_differential tool specification

Tool Information:

  • Name: ExpressionAtlas_search_differential

  • Type: ExpressionAtlasTool

  • Description: Search for differential expression experiments from EBI Expression Atlas. Find experiments where a gene is differentially expressed in disease vs. normal, treated vs. untreated, etc. Supports disease-context expression analysis.

Parameters:

  • gene (string) (optional) Gene symbol or Ensembl ID (e.g., ā€˜TP53ā€™, ā€˜ENSG00000141510ā€™)

  • condition (string) (optional) Condition/disease to filter by (e.g., ā€˜cancerā€™, ā€˜inflammationā€™, ā€˜breastā€™)

  • species (string) (optional) Species name (default: ā€˜homo sapiensā€™)

Example Usage:

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

ExpressionAtlas_search_experiments (Type: ExpressionAtlasTool)Ā¶

Search all EBI Expression Atlas experiments (baseline + differential) by gene and/or condition. Rā€¦

ExpressionAtlas_search_experiments tool specification

Tool Information:

  • Name: ExpressionAtlas_search_experiments

  • Type: ExpressionAtlasTool

  • Description: Search all EBI Expression Atlas experiments (baseline + differential) by gene and/or condition. Returns experiment accessions, types, descriptions, and assay counts. Use to find relevant expression datasets.

Parameters:

  • gene (string) (optional) Gene symbol or Ensembl ID

  • condition (string) (optional) Biological condition or tissue (e.g., ā€˜brainā€™, ā€˜cancerā€™, ā€˜kidneyā€™)

  • species (string) (optional) Species name (optional, e.g., ā€˜homo sapiensā€™)

Example Usage:

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