ArticleNature biotechnology2016
Characterizing genomic alterations in cancer by complementary functional associations.
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Article in Nature biotechnology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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62citing papers in PubMed
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Who cites it
62 citing papers in PubMed.
- Stress adaptation pathways and HA-CD44 signaling maintain the survival of pancreatic cancer cells with centrosome amplification.Cell communication and signaling : CCS · 2026Article
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- Synthetic lethality in cancer drug discovery: challenges and opportunities.Nature reviews. Drug discovery · 2026Review
- Integrated computational and experimental approach to identify Nrf2-regulated molecular targets in cerebral ischemia.Pharmacological reports : PR · 2025Article
- Androgen receptor-mediated regulation of BRCA1 modulates the antioxidant defense in prostate cancer.The Journal of pathology · 2025Article
- Self-amplifying NRF2-EZH2 epigenetic loop converts KRAS-initiated progenitors to invasive pancreatic cancer.Nature cancer · 2025Article
- NRF2 supports non-small cell lung cancer growth independently of CBP/p300-enhanced glutathione synthesis.EMBO reports · 2025Article
- YAP-driven malignant reprogramming of oral epithelial stem cells at single cell resolution.Nature communications · 2025Article
- Evolutionary dependency of cancer mutations in gene pairs inferred by nonsynonymous-synonymous mutation ratios.Genome medicine · 2024Article
- Building a translational cancer dependency map for The Cancer Genome Atlas.Nature cancer · 2024Article
- MicroRNA-367-3p directly targets RAB23 and inhibits proliferation, migration and invasion of bladder cancer cells and increases cisplatin sensitivity.Journal of cancer research and clinical oncology · 2023Article
- Deciphering the Functional Roles of Individual Cancer Alleles Across Comprehensive Cancer Genomic Studies.bioRxiv : the preprint server for biology · 2023Article
- YAP-Driven Malignant Reprogramming of Epithelial Stem Cells at Single Cell Resolution.Research square · 2023Article
- Exploring cell competition for the prevention and therapy of esophageal squamous cell carcinoma.Biochemical pharmacology · 2023Review
- Predicting gene knockout effects from expression data.BMC medical genomics · 2023Article
- Differential regulation of TNFα and IL-6 expression contributes to immune evasion in prostate cancer.Journal of translational medicine · 2022Article
- Identification of a Molecularly-Defined Subset of Breast and Ovarian Cancer Models that Respond to WEE1 or ATR Inhibition, Overcoming PARP Inhibitor Resistance.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- Glutathione peroxidase 2 is a metabolic driver of the tumor immune microenvironment and immune checkpoint inhibitor response.Journal for immunotherapy of cancer · 2022Article
- The β-TrCP-Mediated Pathway Cooperates with the Keap1-Mediated Pathway in Nrf2 DegradationMolecular and cellular biology · 2022Article
- CHMP2A regulates tumor sensitivity to natural killer cell-mediated cytotoxicity.Nature communications · 2022Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
35 authors.
Jong Wook KimEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Olga B BotvinnikEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Omar AbudayyehEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Chet BirgerEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Joseph RosenbluhEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Yashaswi ShresthaEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Mohamed E AbazeedEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Peter S HammermanEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Daniel DiCaraEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
David J KonieczkowskiEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Cory M JohannessenEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Arthur LiberzonEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Amir Reza Alizad-RahvarDepartment of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada.
Gabriela AlexeEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Andrew AguirreEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Mahmoud GhandiEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.ORCID 0000-0003-1897-2265
Heidi GreulichEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Francisca VazquezEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Barbara A WeirEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Eliezer M Van AllenEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Aviad TsherniakEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.ORCID 0000-0002-3797-1877
Diane D ShaoEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Travis I ZackEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Michael NobleEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Gad GetzEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Rameen BeroukhimEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Levi A GarrawayEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Masoud ArdakaniDepartment of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada.
Chiara RomualdiDepartment of Biology, University of Padova, Padova, Italy.
Gabriele SalesDepartment of Biology, University of Padova, Padova, Italy.
David A BarbieEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Jesse S BoehmEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.ORCID 0000-0002-6795-6336
William C HahnEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Jill P MesirovEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Pablo TamayoEli and Edythe Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.ORCID 0000-0002-9360-4668
Funding
VIRAL MALIGNANCYP30CA023100 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DIANE M SIMEONE · 1985 to 2026
$124.9MHarvard Clinical and Translational Science CenterUL1TR001102 · NCATS · HARVARD MEDICAL SCHOOL · PI NADLER, LEE MARSHALL · 2013 to 2017
$106.2MMedical Scientist Training ProgramT32GM007753 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI WALENSKY, LOREN DAVID · 1985 to 2021
$50.0MThe Dana-Farber Cancer Institute Cancer Target Discovery and Development CenterU01CA176058 · NCI · DANA-FARBER CANCER INST · PI HAHN, WILLIAM C. · 2013 to 2021
$7.8MGENOMIC ANALYSIS OF MEDULLOBLASTOMASR01CA109467 · NCI · CHILDREN'S HOSPITAL BOSTON · PI MESIROV, JILL P., POMEROY, SCOTT LOREN · 2004 to 2015
$7.3MSupporting Integrative Genomic Analysis Users with GenePatternR01GM074024 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2005 to 2019
$6.6MMouse Neurodevelopmental Behavior CoreU54HD090255 · NICHD · BOSTON CHILDREN'S HOSPITAL · PI POMEROY, SCOTT LOREN · 2016 to 2020
$5.2MKnowledge-based Gene Expression Analysis for Biomedical and Cancer ResearchR01CA121941 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2006 to 2016
$5.1MEmbryonal Brain Tumor NetworksU01CA184898 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI FRAENKEL, ERNEST, MESIROV, JILL P. · 2014 to 2019
$3.6MGenePattern Notebooks for Cancer ResearchU24CA194107 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2015 to 2019
$2.8MMolecular Signatures to Characterize the Oncogenic State of Individual TumorsR01CA154480 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI TAMAYO, PABLO · 2011 to 2015
$2.0MNCATS NIH HHS UL1 TR001102NCI NIH HHS P30 CA023100NCI NIH HHS R01 CA109467NCI NIH HHS R01 CA121941NCI NIH HHS R01 CA154480NCI NIH HHS U01 CA176058NCI NIH HHS U01 CA184898NCI NIH HHS U24 CA194107NICHD NIH HHS U54 HD090255NIGMS NIH HHS R01 GM074024NIGMS NIH HHS T32 GM007753
Abstract
Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment. We used REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations, demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes.
Indexed as
Biomarkers, TumorChromosome MappingDrug Resistance, NeoplasmGenes, NeoplasmGenetic Predisposition to DiseaseGenome, HumanGenome-Wide Association StudyHumansMutationNeoplasm ProteinsNeoplasmsPolymorphism, Single NucleotideSignal TransductionBiomarkers, TumorNeoplasm Proteins
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.