About the Authors

Erhan Bilal

These first authors contributed equally to this paper, and are listed alphabetically.

Affiliation IBM TJ Watson Research, Yorktown Heights, New York, United States of America

Janusz Dutkowski

These first authors contributed equally to this paper, and are listed alphabetically.

Affiliation Departments of Medicine and Bioengineering, University of California San Diego, La Jolla, California, United States of America

Justin Guinney

These first authors contributed equally to this paper, and are listed alphabetically.

Affiliation Sage Bionetworks, Seattle, Washington, United States of America

In Sock Jang

These first authors contributed equally to this paper, and are listed alphabetically.

Affiliation Sage Bionetworks, Seattle, Washington, United States of America

Benjamin A. Logsdon

These first authors contributed equally to this paper, and are listed alphabetically.

Affiliations Sage Bionetworks, Seattle, Washington, United States of America, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

Gaurav Pandey

These first authors contributed equally to this paper, and are listed alphabetically.

Affiliations Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

Benjamin A. Sauerwine

These first authors contributed equally to this paper, and are listed alphabetically.

Affiliation Sage Bionetworks, Seattle, Washington, United States of America

Yishai Shimoni

These first authors contributed equally to this paper, and are listed alphabetically.

Affiliations Columbia Initiative in Systems Biology, Columbia University, New York, New York, United States of America, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America

Hans Kristian Moen Vollan

These first authors contributed equally to this paper, and are listed alphabetically.

Affiliations Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, The K. G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway, Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom, Department of Oncology, University of Cambridge, Cambridge, United Kingdom, Department of Oncology, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Oslo, Norway

Brigham H. Mecham

Affiliation Sage Bionetworks, Seattle, Washington, United States of America

Oscar M. Rueda

Affiliations Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom, Department of Oncology, University of Cambridge, Cambridge, United Kingdom

Jorg Tost

Affiliation Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA, Institut de Génomique, Evry, France

Christina Curtis

Affiliation Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America

Mariano J. Alvarez

Affiliations Columbia Initiative in Systems Biology, Columbia University, New York, New York, United States of America, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America

Vessela N. Kristensen

Affiliations Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, The K. G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway, Department of Clinical Molecular Biology, Division of Medicine, Akershus University Hospital, Ahus, Norway

Samuel Aparicio

Affiliations Department of Pathology and Laboratory Medicine, University of British Colombia, Vancouver, British Colombia, Canada, Molecular Oncology, British Colombia Cancer Research Center, Vancouver, British Colombia, Canada

Anne-Lise Børresen-Dale

Affiliations Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway, The K. G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway

Carlos Caldas

Affiliations Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom, Department of Oncology, University of Cambridge, Cambridge, United Kingdom, Cambridge Experimental Cancer Medicine Centre, Cambridge, United Kingdom, Cambridge Breast Unit, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, United Kingdom

Andrea Califano

‡ These senior authors contributed equally to this paper.

Affiliations Columbia Initiative in Systems Biology, Columbia University, New York, New York, United States of America, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America, Department of Biomedical Informatics, Columbia University, New York, New York, United States of America, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America, Institute for Cancer Genetics, Columbia University, Columbia University, New York, New York, United States of America, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, United States of America

Stephen H. Friend

‡ These senior authors contributed equally to this paper.

Affiliation Sage Bionetworks, Seattle, Washington, United States of America

Trey Ideker

‡ These senior authors contributed equally to this paper.

Affiliation Departments of Medicine and Bioengineering, University of California San Diego, La Jolla, California, United States of America

Eric E. Schadt

‡ These senior authors contributed equally to this paper.

Affiliation Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

Gustavo A. Stolovitzky

‡ These senior authors contributed equally to this paper.

Affiliation IBM TJ Watson Research, Yorktown Heights, New York, United States of America

Adam A. Margolin

margolin@sagebase.org

‡ These senior authors contributed equally to this paper.

Affiliation Sage Bionetworks, Seattle, Washington, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: E. Bilal, J. Dutkowski, J. Guinney, I.S. Jang, B.A. Logsdon, G. Pandey, B.A. Sauerwine, Y. Shimoni, H.K. Moen Vollan, O.M. Rueda, S. Aparicio, A-L. Borresen-Dale, C. Caldas, A. Califano, S.H. Friend, T. Ideker, E.E. Schadt, G.A. Stolovitzky, A.A. Margolin. Performed the experiments: H.K. Moen Vollan, O.M. Rueda, J. Tost, C. Curtis, V.N. Kristensen, S. Aparicio, A-L. Borresen-Dale, C. Caldas. Analyzed the data: E. Bilal, J. Dutkowski, J. Guinney, I.S. Jang, B.A. Logsdon, G. Pandey, B.A. Sauerwine, Y. Shimoni, B.H. Mecham, M.J. Alvarez, A.A. Margolin. Contributed reagents/materials/analysis tools: H.K. Moen Vollan, O.M. Rueda, J. Tost, V.N. Kristensen, A-L. Borresen-Dale. Wrote the paper: E. Bilal, J. Dutkowski, J. Guinney, I.S. Jang, B.A. Logsdon, G. Pandey, B.A. Sauerwine, Y. Shimoni, H.K. Moen Vollan, V.N. Kristensen, A-L. Borresen-Dale, A.A. Margolin.