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cBioPortal

Web-based resource for researchers to explore, visualize, analyze, and share multidimensional genomics data sets

Direct access to cBioPortal

 

About cBioPortal

The TraIT cBioPortal provides a web-based resource for researchers to explore, visualize, analyze, and share multidimensional cancer genomics data sets as well as other studies with multidimensional genomics data. 

Originally developed at Memorial Sloan Kettering Cancer Center (MSK), the portal became open source in 2011 and is used by tens of thousands of researchers across the globe.

The portal is actively developed and maintained by a multi-institutional team, consisting of MSK, the Dana Farber Cancer Institute, Princess Margaret Cancer Centre in Toronto, Children's Hospital of Philadelphia, The Hyve in the Netherlands, and Bilkent University in Ankara, Turkey.

 

Why cBioPortal

The user-friendly web interface makes visualization of gene-level data across genes, samples and data types available to users, without requiring bioinformatics expertise.

Visualizations include survival analysis, networks analysis, co-expression and the onco-print (gene-print). Furthermore, a study view is available, which provides summary statistics of your clinical data and allows you to create a subset of your data for further analysis.

The portal supports a variety of genomic data types, including somatic mutations, DNA copy-number alterations (CNAs), mRNA and microRNA (miRNA) expression, DNA methylation, protein abundance, and phosphoprotein abundance.

To protect your data, the cBioPortal hosted by TraIT has access policies, meaning that as a study owner you can decide which users have access to your studies.

For further questions regarding this TraIT platform, including requests for usage, please contact the TraIT ServiceDesk.

 

How to start using cBioPortal?

If you are a researcher and would like to see your study data in cBioPortal, the study Principal Investigator (PI) or their delegate should contact the TraIT ServiceDesk. The PI also provides study specific do's and dont's with respect to the use of cBioPortal. Once access is granted to TraIT cBioPortal, you will receive instructions from TraIT. 1st and 2nd line user support is provided via the TraIT ServiceDesk.

The upload of ‘final’ or ‘processed’ data, derived from a data-freeze, will be performed by data Extraction, Transformation and Loading (ETL) experts. If your data is already available in tranSMART, please enter this information in the comments section of the request procedure as this will facilitate import of data in cBioPortal.

If you do not have access yet to the TraIT platform or to the study of interest, please contact the TraIT ServiceDesk at servicedesk@ctmm-trait.nl and request the necessary access.

 

 

References

- Cerami et al: The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data (http://cancerdiscovery.aacrjournals.org/content/2/5/401)
- Gao et al: Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal  (https://www.ncbi.nlm.nih.gov/pubmed/23550210 )