ArticleJournal of the National Cancer Institute2015
Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data.
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Article in Journal of the National Cancer Institute, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17citing papers in PubMed
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Who cites it
17 citing papers in PubMed.
- UALCAN Mobile, an app for cancer proteogenomic data analysis.Research square · 2025Article
- UALCAN Mobile, an app for cancer proteogenomic data analysis.bioRxiv : the preprint server for biology · 2025Article
- X Chromosome Contribution to the Genetic Architecture of Primary Biliary Cholangitis.Gastroenterology · 2021Article
- Converting tabular data into images for deep learning with convolutional neural networks.Scientific reports · 2021Article
- FRMD6 has tumor suppressor functions in prostate cancer.Oncogene · 2021Article
- New Analysis Framework Incorporating Mixed Mutual Information and Scalable Bayesian Networks for Multimodal High Dimensional Genomic and Epigenomic Cancer Data.Frontiers in genetics · 2020Article
- An Oncolytic Adenovirus Targeting Transforming Growth Factor β Inhibits Protumorigenic Signals and Produces Immune Activation: A Novel Approach to Enhance Anti-PD-1 and Anti-CTLA-4 Therapy.Human gene therapy · 2019Article
- A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data.Briefings in bioinformatics · 2019Review
- SLCO4C1 promoter methylation is a potential biomarker for prognosis associated with biochemical recurrence-free survival after radical prostatectomy.Clinical epigenetics · 2019Article
- Imaging-Genomic Study of Head and Neck Squamous Cell Carcinoma: Associations Between Radiomic Phenotypes and Genomic Mechanisms via Integration of The Cancer Genome Atlas and The Cancer Imaging Archive.JCO clinical cancer informatics · 2019Article
- Article
- TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data.Bioinformatics (Oxford, England) · 2018Article
- RHCG and TCAF1 promoter hypermethylation predicts biochemical recurrence in prostate cancer patients treated by radical prostatectomy.Oncotarget · 2017Article
- CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms.Nucleic acids research · 2016Article
- Deciphering Genomic Underpinnings of Quantitative MRI-based Radiomic Phenotypes of Invasive Breast Carcinoma.Scientific reports · 2015Article
- Ubiquitin-specific protease 12 interacting partners Uaf-1 and WDR20 are potential therapeutic targets in prostate cancer.Oncotarget · 2015Article
- High levels of 5-hydroxymethylcytosine (5hmC) is an adverse predictor of biochemical recurrence after prostatectomy in ERG-negative prostate cancer.Clinical epigenetics · 2015Article
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Authors and funding
15 authors.
Yitan ZhuProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Yanxun XuProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Donald L HelsethProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Kamalakar GulukotaProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Shengjie YangProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Lorenzo L PesceProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Riten MitraProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Peter MüllerProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Subhajit SenguptaProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Wentian GuoProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Jonathan C SilversteinProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Ian FosterProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Nigel ParsadProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Kevin P WhiteProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL.
Yuan JiProgram of Computational Genomics & Medicine (YZ, SY, SS, YJ), Center for Molecular Medicine (DLH Jr, KG), and Center for Biomedical Research Informatics (JCS, NP), NorthShore University HealthSystem, Evanston, IL; Department of Mathematics, The University of Texas at Austin, Austin, TX (YX, PM); Computation Institute (LLP, IF) and Institute for Genomics and Systems Biology (KPW), The University of Chicago and Argonne National Laboratory, Chicago IL; Department of Bioinformatics & Biostatistics, University of Louisville, Louisville, KY (RM); School of Public Health, Fudan University, Shanghai, P. R. China (WG); Department of Human Genetics and Department of Ecology & Evolution (KPW) and Department of Public Health Sciences (YJ), The University of Chicago, Chicago, IL. koaeraser@gmail.com.
Funding
Beagle: A Supercomputer for Computational Biology, Simulation, and Data AnalysisS10RR029030 · NCRR · UNIVERSITY OF CHICAGO · PI FOSTER, IAN · 2010 to 2010
$7.0MBayesian models for cancer prognosis by integrating diverse types of dataR01CA132897 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI JI, YUAN, MUELLER, PETER · 2008 to 2019
$2.1MNCI NIH HHS R01 CA132897NCRR NIH HHS S10 RR029030-01
Abstract
backgroundGenetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer.
methodsWe introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood model derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes "Prior interaction map + TCGA data → Posterior interaction map."
resultsZodiac provides molecular interactions for about 200 million pairs of genes. All the results are generated from a big-data analysis and organized into a comprehensive database allowing customized search. In addition, Zodiac provides data processing and analysis tools that allow users to customize the prior networks and update the genetic pathways of their interest. Zodiac is publicly available at www.compgenome.org/ZODIAC.
conclusionsZodiac recapitulates and extends existing knowledge of molecular interactions in cancer. It can be used to explore novel gene-gene interactions, transcriptional regulation, and other types of molecular interplays in cancer.
Indexed as
Databases, GeneticEpistasis, GeneticGenomicsSoftwareBayes TheoremHumansInternetLikelihood FunctionsNeoplasmsUser-Computer Interface
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