About the Authors

Thomas W. Chittenden

Affiliations Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America, Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America, Department of Statistics, Oxford Centre for Gene Function, University of Oxford, Oxford, United Kingdom

Jane Pak

Affiliation Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America

Renee Rubio

Affiliation Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America

Hailing Cheng

Affiliation Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States America

Kristina Holton

Affiliation Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America

Niall Prendergast

Affiliation Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America

Vladimir Glinskii

Affiliation Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America

Yi Cai

Affiliation Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America

Aedin Culhane

Affiliations Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America, Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America

Stefan Bentink

Affiliations Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America, Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America

Mathew Schwede

Affiliation Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America

Jessica C. Mar

Affiliations Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America, Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America

Eleanor A. Howe

Affiliations Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America, Department of Statistics, Oxford Centre for Gene Function, University of Oxford, Oxford, United Kingdom

Martin Aryee

Affiliation Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States America

Razvan Sultana

Affiliation Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America

Anthony A. Lanahan

Affiliation Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, United States America

Jennifer M. Taylor

Affiliation CSIRO Plant Industry, Canberra, Australia

Chris Holmes

Affiliations Department of Statistics, Oxford Centre for Gene Function, University of Oxford, Oxford, United Kingdom, Mammalian Genetics Unit, Medical Research Council Harwell, Oxfordshire, United Kingdom

William C. Hahn

Affiliations Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States America

Jean J. Zhao

Affiliation Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States America

J. Dirk Iglehart

Affiliation Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States America

John Quackenbush

johnq@jimmy.harvard.edu

Affiliations Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America, Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: TWC JQ. Performed the experiments: TWC JP HC. Analyzed the data: TWC AC SB. Contributed reagents/materials/analysis tools: HC JJZ. Wrote the paper: TWC JMT CH WCH JJZ JDI JQ. Responsible for all experimental work, data analysis, and project planning: TWC. Provided technical support for experiments: JP RR KH NP VG YC AAL. Performed soft agar assays: HC. Generated and analyzed breast and ovarian cancer datasets: AC MS. Generated and analyzed the oncogenic pathway dataset: SB. Provided intellectual input and assisted in the development and maintenance of the nEASE algorithm: JCM EAH MA. Built and maintained gene ontology annotation files: RS. Provided intellectual input regarding conception of bioinformatics and statistical approaches: JMT CH JQ. Provided intellectual input regarding conception and implementation of the experimental design for this study: WCH JJZ JDI JQ.