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Abstract

The cBioPortal for Cancer Genomics (http://cbioportal.org) provides 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. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.

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Supplementary Material

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References and Notes

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Acknowledgments

We thank R. Sheridan (Sander Lab, MSKCC), J. Barlin (Levine Lab, MSKCC), and P. Jelinic (Levine Lab, MSKCC) for invaluable feedback to improve the usability of the portal. We thank our collaborators at MSKCC and in the TCGA and the Stand Up To Cancer (SU2C) research networks, including D. Levine, D. Solit, C. Brennan (MSKCC); B. S. Taylor (UCSF); G. Mills (MD Anderson); and K. Shaw (NCI), for generous feedback and links to the cancer genomics community. We thank G. Bader and M. Franz (University of Toronto) for support with Cytoscape Web and the entire Pathway Commons team (MSKCC and University of Toronto) for developing the Pathway Commons Web Application Programming Interface (API) and the network download facility. We thank J. Zhu (UCSC) and N. Lopez-Bigas (University Pompeu Fabra) for feedback regarding the UCSC Cancer Genome Browser and IntOGen. E.C. is now at Blueprint Medicines in Cambridge. B.A.A. is in the Tri-Institutional Training Program in Computational Biology and Medicine, a joint graduate program of MSKCC, Cornell University, and Weill Cornell Medical College. Funding: The cBioPortal for Cancer Genomics is supported by NCI as part of the TCGA Genome Data Analysis Center grant, NCI-U24CA143840, and NCI-R21CA135870. Funding for a separate Stand Up To Cancer (SU2C) instance of the cBioPortal is provided by a Stand Up To Cancer Dream Team Translational Research Grant, a Program of the Entertainment Industry Foundation (SU2C-AACR-DT0209). Funding for network visualization and analysis within the portal is provided by the National Resource for Network Biology (NIH National Center for Research Resources grant numbers P41 RR031228 and GM103504). Funding for MutationAssessor is from the NIH NCI R01 CA132744. Funding for the integration with the Integrative Genomics Viewer (IGV) is provided by the Starr Cancer Consortium (I5-A500). Competing interests: The authors declare that they have no competing interests.

Authors

Affiliations

Jianjiong Gao
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Bülent Arman Aksoy
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Ugur Dogrusoz
Computer Engineering Department, Bilkent University, 06800 Ankara, Turkey.
Gideon Dresdner
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Benjamin Gross
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
S. Onur Sumer
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Yichao Sun
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Anders Jacobsen
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Rileen Sinha
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Erik Larsson
Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden.
Ethan Cerami
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Blueprint Medicines, Cambridge, MA 02142, USA.
Chris Sander
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
Nikolaus Schultz
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

Notes

Correspondence should be addressed to [email protected]; user support is available at [email protected]

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