cBioPortal Database

cBioPortal Database

Overview

cBioPortal for Cancer Genomics is a public repository of cancer genomics data including TCGA, ICGC, and hundreds of curated studies spanning 100+ cancer types. It provides somatic mutation profiles, copy number alterations (CNA), gene expression, clinical data (survival, stage, treatment history), and methylation data for tens of thousands of patient samples. Data is accessible via a REST API at https://www.cbioportal.org/api/ with no authentication required.

When to Use

• Retrieving somatic mutation profiles (variant type, amino acid change) for a gene across TCGA studies
• Querying copy number alteration data (amplification, deep deletion) for candidate cancer driver genes
• Accessing clinical data — overall survival, disease-free survival, tumor stage — for survival curve analysis
• Identifying which cancer studies have molecular profiling data for a specific cancer type (e.g., breast, lung)
• Downloading gene expression (RNA-seq FPKM/RSEM) data from specific TCGA cohorts for differential expression analysis
• Correlating genomic alterations with clinical outcomes in a specific study
• Use omics-plotting SKILL to render bar charts, mutation-frequency heatmaps, and Kaplan–Meier curves from the query results
• Use gnomad-database instead when you need population-level variant allele frequencies in healthy individuals
• For drug-gene interaction lookups use opentargets-database; cBioPortal provides the genomic alteration data, not drug interaction annotations

Prerequisites

• Python packages: requests, pandas, matplotlib
• Data requirements: Entrez gene symbols (e.g., TP53), cBioPortal study IDs (e.g., tcga_brca), molecular profile IDs
• Environment: internet connection; no API key required
• Rate limits: no strict rate limits; use time.sleep(0.2) between batch requests for polite access

pip install requests pandas matplotlib

Quick Start

import requests
import pandas as pd

BASE_URL = "https://www.cbioportal.org/api"

def cbio_get(endpoint, params=None):
    """GET request to cBioPortal REST API, returns parsed JSON."""
    r = requests.get(f"{BASE_URL}/{endpoint}", params=params,