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cBioPortal for Cancer Genomics is an open-access web resource for exploring, visualizing and analyzing multidimensional cancer genomics data. This page is for researchers deciding whether cBioPortal fits their question, which of its several public instances to use, what the Results View tabs do, and how to cite it. The facts below come from the project’s own documentation and the three publications it lists, checked 2026-11-07.
What cBioPortal is
The 2013 Science Signaling paper by Gao and colleagues describes cBioPortal as a web resource for exploring, visualizing and analyzing multidimensional cancer genomics data, covering genetic, epigenetic, gene expression and proteomic events. It supports survival analysis, patient-centric queries and programmatic access, and is designed so that users do not need bioinformatics expertise. The original 2012 Cancer Discovery paper by Cerami and colleagues introduced it as an open-access resource for interactive exploration of such data; at that time it held more than 5,000 tumor samples from 20 cancer studies (a 2012 figure, not a current count).
It is also software. The documentation says the code is available under an open source license via GitHub (github.com/cbioportal/cbioportal), so institutions can run their own instance with their own data.
Who runs it and what it covers
According to the project’s About page, the software is developed and maintained by a multi-institutional team: Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Princess Margaret Cancer Centre, Children’s Hospital of Philadelphia, The Hyve, SE4BIO and Bilkent University. The main public site is hosted by the Center for Molecular Oncology at Memorial Sloan Kettering. Funders named on the page include the National Cancer Institute (through the ITCR and HTAN programs), the MSK Kravis Center, Dana-Farber, the American Association for Cancer Research (for Project GENIE), Break Through Cancer and the Gray Foundation.
The data is organized into studies, each contributed by a project or institution. The public portal hosts data from large programs such as The Cancer Genome Atlas (TCGA). Terms of reuse are set per study and source, so check the study’s own description and publication before redistributing or combining data. For a comparison of where TCGA data is distributed from, see Genomic Data Commons (GDC).
Which instance? A map of the cBioPortal family
Because the software is open source, “cBioPortal” can mean several different sites. The instances below are the ones named in the documentation and operated by the project’s partners:
| Instance | What it is |
|---|---|
| Public portal (cbioportal.org) | Hosted by the MSK Center for Molecular Oncology; the general-purpose site for public cancer genomics studies. |
| AACR Project GENIE (genie.cbioportal.org) | An international registry from 19 cancer centers; the 2023 Cancer Research paper reports more than 130,000 patients with data made public through this site, plus longitudinal BPC data on 25,000 patients (several thousand of them in cBioPortal). |
| CCDI cBioPortal | An instance run for the Childhood Cancer Data Initiative (CCDI) at cbioportal.ccdi.cancer.gov, set up so users can explore and analyze data without downloading or processing large datasets. |
| PDX portal at The Jackson Laboratory | A separate cBioPortal instance at cbioportal.informatics.jax.org, a Jackson Laboratory domain, presented as cBioPortal for patient-derived xenograft (PDX) cancer genomics. |
The practical consequence: the instance you used is part of your methods. Record which site, which study identifiers and the date you accessed them.
Using the interface
The user guide is organized by role (portal user, API user, instance maintainer, developer) and documents the interface by page. The terms below are the ones the documentation uses.
- Study View summarizes a single study, and supports building virtual studies from selected samples.
- Group Comparison compares defined sets of samples or patients.
- Query / Results View runs a gene-centric query across one or more studies. The results page is split into tabs.
- Patient View shows the data for one patient.
- Onco Query Language (OQL) lets you specify the alterations you want to match for each gene in a query.
Results View tabs
The user guide lists these Results View tabs: OncoPrint, Cancer Types Summary, Mutual Exclusivity, Plots, Mutations, Co-expression, Comparison/Survival, CN Segments, Pathways and Downloads. The guide’s page index links each tab to tutorial slides and a recorded webinar, and the Mutations tab also has a how-to video on filtering and adding clinical data. Survival analysis is one of the capabilities the 2013 paper describes. Work through the tutorial slides for the tab you need rather than relying on a summary here.
For file formats if you plan to load your own data into a self-hosted instance, the documentation has a dedicated File Formats section. Programmatic access is covered under API documentation, and the docs mention a “How to download data” video and an “API and R Client” webinar. The sign-in and account options, where an instance offers them, are on the instance itself.
How to cite cBioPortal
The documentation’s overview page lists three publications. Cite the portal papers and, separately, the paper for each study whose data you analyzed (editorial advice, consistent with how repository citation works generally).
- Cerami E, et al. Cancer Discovery. 2012 May;2(5):401-404. doi:10.1158/2159-8290.CD-12-0095. PMID 22588877.
- Gao J, et al. Science Signaling. 2013 Apr 2;6(269):pl1. doi:10.1126/scisignal.2004088. PMID 23550210.
- de Bruijn I, et al. Cancer Research. 2023 Dec 1;83(23):3861-3867. doi:10.1158/0008-5472.CAN-23-0816. PMID 37668528.
The third paper is the one most relevant when you use GENIE or the longitudinal BPC data.
Strengths and limits
Strengths (as documented). Open access; no bioinformatics expertise needed for common queries; combines several data types in one query; programmatic access and a self-hostable open source codebase; an active multi-institution maintainer group.
Limits (editorial interpretation).
- It is an exploration and visualization layer, not a substitute for the original data source when you need the full primary data, controlled-access records or a specific data release; for access rules see the NIH Genomic Data Sharing policy.
- Study contents change as studies are added or updated, so a figure you read today may differ later. Record the date and study identifiers.
- Reuse terms differ by study; do not assume one license for the whole portal.
Alternatives and related resources
| Resource | Relationship |
|---|---|
| Genomic Data Commons | A data repository for the underlying NCI genomic data, including TCGA, rather than an exploration portal. |
| TCGA | A major program whose data appears in cBioPortal studies. |
| Domain repositories in general | The category cBioPortal’s data sources belong to; see also data repository. |
Frequently asked questions
Is cBioPortal a database?
It is a web portal and open source software layered over study datasets that are loaded into a database. The documentation includes a File Formats section describing how study data is structured for loading.
Where is the cBioPortal code on GitHub?
At https://github.com/cbioportal/cbioportal, the source repository the documentation points to.
Does cBioPortal include TCGA data?
Yes, the public portal hosts data from large programs such as TCGA; see the TCGA entry for what the program is.
How do I cite cBioPortal?
Use the three references in the citation section above, and add the primary publication of each study you analyzed.
Sources
All links checked 2026-11-07.
- cBioPortal documentation home: https://docs.cbioportal.org/
- About us: https://docs.cbioportal.org/about-us/
- User guide overview (publications list): https://docs.cbioportal.org/user-guide/overview/
- User guide by page: https://docs.cbioportal.org/user-guide/by-page/
- Cerami E, et al. 2012, Cancer Discovery: https://pubmed.ncbi.nlm.nih.gov/22588877/
- Gao J, et al. 2013, Science Signaling: https://pubmed.ncbi.nlm.nih.gov/23550210/
- de Bruijn I, et al. 2023, Cancer Research: https://pubmed.ncbi.nlm.nih.gov/37668528/
- AACR Project GENIE portal: https://genie.cbioportal.org/
- CCDI cBioPortal: https://cbioportal.ccdi.cancer.gov/
