Intogen Tools

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

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

Available Tools

IntOGen_get_drivers (Type: IntOGenTool)

Get cancer driver genes for a specific cancer type from IntOGen. Returns genes identified as driv…

IntOGen_get_drivers tool specification

Tool Information:

  • Name: IntOGen_get_drivers

  • Type: IntOGenTool

  • Description: Get cancer driver genes for a specific cancer type from IntOGen. Returns genes identified as drivers by computational methods (dNdScv, OncodriveFML, OncodriveCLUSTL, HotMAPS, smRegions, CBaSE, MutPanning) applied to somatic mutation data from thousands of tumors. Each result includes the gene symbol, number of mutations and mutated samples across cohorts. Use IntOGen_list_cancer_types to see available cancer type codes. Example: cancer_type=’BRCA’ returns 118 driver genes for breast cancer including TP53, PIK3CA, GATA3.

Parameters:

  • cancer_type (string) (required) IntOGen cancer type code. Examples: ‘BRCA’ (breast), ‘LUAD’ (lung adenocarcinoma), ‘COADREAD’ (colorectal), ‘AML’ (acute myeloid leukemia), ‘SKCM’ (melanoma), ‘GBM’ (glioblastoma). Use IntOGen_list_cancer_types to see all available codes.

Example Usage:

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

IntOGen_get_gene_info (Type: IntOGenTool)

Get driver gene classification for a specific gene across all cancer types from IntOGen. Returns …

IntOGen_get_gene_info tool specification

Tool Information:

  • Name: IntOGen_get_gene_info

  • Type: IntOGenTool

  • Description: Get driver gene classification for a specific gene across all cancer types from IntOGen. Returns the list of cancer types where the gene is identified as a cancer driver, along with the detection methods used (dNdScv, OncodriveFML, OncodriveCLUSTL, HotMAPS, smRegions, CBaSE, MutPanning) and mutation statistics. Example: gene=’TP53’ is a driver in 74 cancer types; gene=’KRAS’ is a driver in 22 cancer types.

Parameters:

  • gene (string) (required) Gene symbol (HUGO nomenclature). Examples: ‘TP53’, ‘KRAS’, ‘PIK3CA’, ‘BRAF’, ‘EGFR’, ‘PTEN’, ‘APC’, ‘BRCA1’, ‘IDH1’, ‘NRAS’.

Example Usage:

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

IntOGen_list_cancer_types (Type: IntOGenTool)

List all 87 cancer types available in IntOGen with their codes and full names. Returns cancer typ…

IntOGen_list_cancer_types tool specification

Tool Information:

  • Name: IntOGen_list_cancer_types

  • Type: IntOGenTool

  • Description: List all 87 cancer types available in IntOGen with their codes and full names. Returns cancer type identifiers (e.g., BRCA, LUAD, COADREAD, AML, SKCM) that can be used with IntOGen_get_drivers and IntOGen_list_cohorts. IntOGen covers 87 cancer types spanning solid tumors, hematological malignancies, and pediatric cancers.

Parameters:

No parameters required.

Example Usage:

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

IntOGen_list_cohorts (Type: IntOGenTool)

List available cancer cohorts from IntOGen with sample counts and tumor types. Returns cohort IDs…

IntOGen_list_cohorts tool specification

Tool Information:

  • Name: IntOGen_list_cohorts

  • Type: IntOGenTool

  • Description: List available cancer cohorts from IntOGen with sample counts and tumor types. Returns cohort IDs, names, data sources (TCGA, ICGC, Hartwig, etc.), sample counts, tumor type (Primary/Metastasis), and age group (Adult/Pediatric). Optionally filter by cancer type. IntOGen includes 271 cohorts from major genomic studies. Example: cancer_type=’BRCA’ returns 14 breast cancer cohorts from TCGA, Hartwig, ICGC, and others.

Parameters:

  • cancer_type ([‘string’, ‘null’]) (optional) Optional cancer type code to filter cohorts. If omitted, returns all 271 cohorts. Examples: ‘BRCA’, ‘LUAD’, ‘COADREAD’.

Example Usage:

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