Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Subscribe

Sci. Signal., 2 April 2013
Vol. 6, Issue 269, p. pl1
[DOI: 10.1126/scisignal.2004088]

PROTOCOLS

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

Jianjiong Gao1, Bülent Arman Aksoy1 , Ugur Dogrusoz2 , Gideon Dresdner1 , Benjamin Gross1 , S. Onur Sumer1 , Yichao Sun1 , Anders Jacobsen1 , Rileen Sinha1 , Erik Larsson3 , Ethan Cerami1,4 , Chris Sander1, and Nikolaus Schultz1

1 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
2 Computer Engineering Department, Bilkent University, 06800 Ankara, Turkey.
3 Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, S-405 30 Gothenburg, Sweden.
4 Blueprint Medicines, Cambridge, MA 02142, USA.

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.

Correspondence should be addressed to cbioportal{at}cbio.mskcc.org; user support is available at cbioportal{at}googlegroups.com

Citation: J. Gao, B. A. Aksoy, U. Dogrusoz, G. Dresdner, B. Gross, S. O. Sumer, Y. Sun, A. Jacobsen, R. Sinha, E. Larsson, E. Cerami, C. Sander, N. Schultz, Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal. Sci. Signal. 6, pl1 (2013).

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles.
B. A. Aksoy, E. Demir, O. Babur, W. Wang, X. Jing, N. Schultz, and C. Sander (2014)
Bioinformatics
   Abstract »    Full Text »    PDF »
Association of the Breast Cancer Antiestrogen Resistance Protein 1 (BCAR1) and BCAR3 Scaffolding Proteins in Cell Signaling and Antiestrogen Resistance.
Y. Wallez, S. J. Riedl, and E. B. Pasquale (2014)
J. Biol. Chem. 289, 10431-10444
   Abstract »    Full Text »    PDF »
RNA editing in RHOQ promotes invasion potential in colorectal cancer.
S.-W. Han, H.-P. Kim, J.-Y. Shin, E.-G. Jeong, W.-C. Lee, K. Y. Kim, S. Y. Park, D.-W. Lee, J.-K. Won, S.-Y. Jeong, et al. (2014)
J. Exp. Med. 211, 613-621
   Abstract »    Full Text »    PDF »
Detection of a Recurrent DNAJB1-PRKACA Chimeric Transcript in Fibrolamellar Hepatocellular Carcinoma.
J. N. Honeyman, E. P. Simon, N. Robine, R. Chiaroni-Clarke, D. G. Darcy, I. I. P. Lim, C. E. Gleason, J. M. Murphy, B. R. Rosenberg, L. Teegan, et al. (2014)
Science 343, 1010-1014
   Abstract »    Full Text »    PDF »
Cyclin E1 Deregulation Occurs Early in Secretory Cell Transformation to Promote Formation of Fallopian Tube-Derived High-Grade Serous Ovarian Cancers.
A. M. Karst, P. M. Jones, N. Vena, A. H. Ligon, J. F. Liu, M. S. Hirsch, D. Etemadmoghadam, D. D. L. Bowtell, and R. Drapkin (2014)
Cancer Res. 74, 1141-1152
   Abstract »    Full Text »    PDF »
The Molecular Balancing Act of p16INK4a in Cancer and Aging.
K. M. LaPak and C. E. Burd (2014)
Mol. Cancer Res. 12, 167-183
   Abstract »    Full Text »    PDF »
Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of Squamous Cell Carcinomas.
D. Schramek, A. Sendoel, J. P. Segal, S. Beronja, E. Heller, D. Oristian, B. Reva, and E. Fuchs (2014)
Science 343, 309-313
   Abstract »    Full Text »    PDF »
Genome-wide Profiling of Genetic Synthetic Lethality Identifies CDK12 as a Novel Determinant of PARP1/2 Inhibitor Sensitivity.
I. Bajrami, J. R. Frankum, A. Konde, R. E. Miller, F. L. Rehman, R. Brough, J. Campbell, D. Sims, R. Rafiq, S. Hooper, et al. (2014)
Cancer Res. 74, 287-297
   Abstract »    Full Text »    PDF »
DriverDB: an exome sequencing database for cancer driver gene identification.
W.-C. Cheng, I.-F. Chung, C.-Y. Chen, H.-J. Sun, J.-J. Fen, W.-C. Tang, T.-Y. Chang, T.-T. Wong, and H.-W. Wang (2014)
Nucleic Acids Res. 42, D1048-D1054
   Abstract »    Full Text »    PDF »
Integrin {alpha}3{beta}1 Can Function to Promote Spontaneous Metastasis and Lung Colonization of Invasive Breast Carcinoma.
B. Zhou, K. N. Gibson-Corley, M. E. Herndon, Y. Sun, E. Gustafson-Wagner, M. Teoh-Fitzgerald, F. E. Domann, M. D. Henry, and C. S. Stipp (2014)
Mol. Cancer Res. 12, 143-154
   Abstract »    Full Text »    PDF »
Mitogen-activated Protein Kinase Signaling Mediates Phosphorylation of Polycomb Ortholog Cbx7.
H.-a. Wu, J. L. Balsbaugh, H. Chandler, A. Georgilis, H. Zullow, J. Shabanowitz, D. F. Hunt, J. Gil, G. Peters, and E. Bernstein (2013)
J. Biol. Chem. 288, 36398-36408
   Abstract »    Full Text »    PDF »
Using Functional Signature Ontology (FUSION) to Identify Mechanisms of Action for Natural Products.
M. B. Potts, H. S. Kim, K. W. Fisher, Y. Hu, Y. P. Carrasco, G. B. Bulut, Y.-H. Ou, M. L. Herrera-Herrera, F. Cubillos, S. Mendiratta, et al. (2013)
Science Signaling 6, ra90
   Abstract »    Full Text »    PDF »
Low-copy piggyBac transposon mutagenesis in mice identifies genes driving melanoma.
T. K. Ni, S. F. Landrette, R. D. Bjornson, M. W. Bosenberg, and T. Xu (2013)
PNAS 110, E3640-E3649
   Abstract »    Full Text »    PDF »

To Advertise     Find Products


Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882