Overview
What It Is
The cBioPortal for Cancer Genomics is a web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. It was originally developed at Memorial Sloan Kettering Cancer Center (MSK) and is open-source and freely accessible. PubMed Central
Scale
Initially containing 5 published datasets and 15 provisional TCGA datasets, cBioPortal now contains data on over 100,000 tumor samples from nearly 300 studies across dozens of cancer types and is maintained as an open-source resource. American Association for Cancer Research
Data Types
Genomic data types integrated by cBioPortal include somatic mutations, DNA copy-number alterations, mRNA and microRNA expression, DNA methylation, protein abundance, and phosphoprotein abundance. More recent integrations have added CPTAC mass spectrometry proteomics, structural variants, and tumor mutational signatures. PubMed Central
Key Datasets
Major data sources include all TCGA pan-cancer studies, ICGC, MSK-IMPACT (the large institutional sequencing program at MSK), GENIE BPC, the Cancer Cell Line Encyclopedia (CCLE), and numerous disease-specific studies from institutions worldwide. Recent additions include TARGET pediatric cancer studies from the NCI Genomic Data Commons, and new datasets such as a Mixed Tumors cohort of over 5,000 samples.
Key Features
The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and programmatic access via API. The intuitive web interface makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise.
Specific tools include the OncoPrint (a compact visual summary of genomic alterations across a cohort), mutation mapper, co-expression analysis, pathway enrichment, and the ability to define and compare virtual cohorts. Users can also upload and visualize their own private data.
Governance & Access
The cBioPortal software is available under an open-source license via GitHub, and the public site is hosted by the Center for Molecular Oncology at MSK. Most data is freely accessible without login, though some controlled-access datasets (like GENIE BPC) require registration and agreement to terms. Institutions like UCSF, Dana-Farber, and others have also deployed their own local instances with institutional clinical sequencing data.
Relevance to Gynecologic Oncology
cBioPortal is particularly useful for ovarian, endometrial, and cervical cancer research, as it hosts all TCGA gynecologic tumor datasets with integrated multi-omic data, GENIE registry data, and serves as the primary public access point for AOCS and GENIE BPC data. It has been cited in thousands of publications and is widely considered an essential resource for translational cancer genomics research.
Notes
Recommended first stop for non-bioinformaticians. Also hosts AACR GENIE and MSK-IMPACT ovarian studies. No raw sequencing files.