Cancer Prognosis Tools

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

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

Available Tools

CancerPrognosis_get_gene_expression (Type: CancerPrognosisTool)

Fetch gene expression values (RNA-seq) for a specific gene across cancer samples in a TCGA or cBi…

CancerPrognosis_get_gene_expression tool specification

Tool Information:

  • Name: CancerPrognosis_get_gene_expression

  • Type: CancerPrognosisTool

  • Description: Fetch gene expression values (RNA-seq) for a specific gene across cancer samples in a TCGA or cBioPortal study. Returns per-sample expression values with summary statistics (mean, median, min, max). Output can be combined with survival data for expression-based prognostic analysis. Supports 33 TCGA cancer types and any cBioPortal study with mRNA expression data.

Parameters:

  • operation (string) (optional) Operation type

  • cancer (string) (optional) TCGA cancer type abbreviation (e.g., ‘BRCA’, ‘LUAD’, ‘COADREAD’) or cBioPortal study ID. Use cancer_type as alias.

  • cancer_type (string) (optional) Alias for cancer. TCGA cancer type (e.g., ‘BRCA’, ‘LUAD’, ‘COADREAD’) or cBioPortal study ID.

  • study_id (string) (optional) Alias for cancer. cBioPortal study ID (e.g., ‘brca_tcga’, ‘luad_tcga’).

  • gene (string) (optional) Gene symbol (e.g., ‘TP53’, ‘BRCA1’, ‘EGFR’, ‘CD8A’)

  • gene_symbol (string) (optional) Alias for gene. Gene symbol (e.g., ‘TP53’, ‘BRCA1’, ‘EGFR’).

  • gene_name (string) (optional) Alias for gene. Gene symbol or name (e.g., ‘TP53’, ‘BRCA1’).

  • max_samples ([‘integer’, ‘null’]) (optional) Upper bound on sample records to return (default 500, max 2000). Actual count may be lower if some samples lack expression data for the requested gene.

Example Usage:

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

CancerPrognosis_get_study_summary (Type: CancerPrognosisTool)

Get summary information for a cancer study including available molecular profiles (mutations, exp…

CancerPrognosis_get_study_summary tool specification

Tool Information:

  • Name: CancerPrognosis_get_study_summary

  • Type: CancerPrognosisTool

  • Description: Get summary information for a cancer study including available molecular profiles (mutations, expression, CNV), survival-related clinical attributes, and sample counts. Useful for determining what data is available before querying expression or survival data. Lists all 33 supported TCGA cancer type abbreviations.

Parameters:

  • operation (string) (optional) Operation type

  • cancer (string) (optional) TCGA cancer type abbreviation (e.g., ‘BRCA’, ‘LUAD’, ‘COADREAD’) or cBioPortal study ID. Use cancer_type as alias.

  • cancer_type (string) (optional) Alias for cancer. TCGA cancer type abbreviation (e.g., ‘BRCA’, ‘LUAD’, ‘COADREAD’).

  • study_id (string) (optional) Alias for cancer. cBioPortal study ID (e.g., ‘brca_tcga’, ‘luad_tcga’).

Example Usage:

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

CancerPrognosis_get_survival_data (Type: CancerPrognosisTool)

Retrieve patient-level overall survival (OS) and disease-free survival (DFS) data from a TCGA or …

CancerPrognosis_get_survival_data tool specification

Tool Information:

  • Name: CancerPrognosis_get_survival_data

  • Type: CancerPrognosisTool

  • Description: Retrieve patient-level overall survival (OS) and disease-free survival (DFS) data from a TCGA or cBioPortal cancer study. Returns per-patient survival times, event status, and age. Data can be directly used with Survival_kaplan_meier or Survival_log_rank_test tools for custom survival analyses. Supports 33 TCGA cancer types (BRCA, LUAD, COAD, GBM, etc.) and 400+ cBioPortal studies.

Parameters:

  • operation (string) (optional) Operation type

  • cancer (string) (optional) TCGA cancer type abbreviation (e.g., ‘BRCA’, ‘LUAD’, ‘COAD’, ‘GBM’, ‘COADREAD’) or cBioPortal study ID (e.g., ‘brca_tcga’). Use cancer_type as alias.

  • cancer_type (string) (optional) Alias for cancer. TCGA cancer type abbreviation (e.g., ‘BRCA’, ‘LUAD’, ‘COAD’, ‘GBM’, ‘COADREAD’) or cBioPortal study ID.

  • study_id (string) (optional) Alias for cancer. cBioPortal study ID (e.g., ‘brca_tcga’, ‘coadread_tcga’, ‘luad_tcga’).

  • max_patients ([‘integer’, ‘null’]) (optional) Maximum number of patient records to return (default 500, max 2000)

Example Usage:

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

CancerPrognosis_search_studies (Type: CancerPrognosisTool)

Search cBioPortal for cancer genomics studies by keyword. Find studies by cancer type, institutio…

CancerPrognosis_search_studies tool specification

Tool Information:

  • Name: CancerPrognosis_search_studies

  • Type: CancerPrognosisTool

  • Description: Search cBioPortal for cancer genomics studies by keyword. Find studies by cancer type, institution, or data type. Returns study IDs that can be used with other CancerPrognosis tools. Covers 400+ studies including all TCGA projects, AACR GENIE, MSK-IMPACT, and institutional cohorts.

Parameters:

  • operation (string) (optional) Operation type

  • keyword (string) (optional) Search keyword (e.g., ‘breast’, ‘lung’, ‘TCGA’, ‘melanoma’, ‘glioblastoma’)

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return (default 20, max 100)

  • cancer_type (string) (optional) Cancer type to search for. Alias for keyword.

  • cancer (string) (optional) Cancer type to search for. Alias for keyword.

  • query (string) (optional) Search query. Alias for keyword (e.g., ‘lung’, ‘breast’, ‘TCGA’).

Example Usage:

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