title: Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data.
abstract: BACKGROUND
  Genetic 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.
  
  
  METHODS
  We 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."
  
  
  RESULTS
  Zodiac 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.
  
  
  CONCLUSIONS
  Zodiac 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.
authors.affiliation: Program 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.
authors.forename: Yitan
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Program 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.
authors.forename: Yanxun
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Program 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.
authors.forename: Donald L
authors.initials: DL
authors.lastname: Helseth
authors.affiliation: Program 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.
authors.forename: Kamalakar
authors.initials: K
authors.lastname: Gulukota
authors.affiliation: Program 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.
authors.forename: Shengjie
authors.initials: S
authors.lastname: Yang
authors.affiliation: Program 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.
authors.forename: Lorenzo L
authors.initials: LL
authors.lastname: Pesce
authors.affiliation: Program 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.
authors.forename: Riten
authors.initials: R
authors.lastname: Mitra
authors.affiliation: Program 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.
authors.forename: Peter
authors.initials: P
authors.lastname: Müller
authors.affiliation: Program 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.
authors.forename: Subhajit
authors.initials: S
authors.lastname: Sengupta
authors.affiliation: Program 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.
authors.forename: Wentian
authors.initials: W
authors.lastname: Guo
authors.affiliation: Program 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.
authors.forename: Jonathan C
authors.initials: JC
authors.lastname: Silverstein
authors.affiliation: Program 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.
authors.forename: Ian
authors.initials: I
authors.lastname: Foster
authors.affiliation: Program 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.
authors.forename: Nigel
authors.initials: N
authors.lastname: Parsad
authors.affiliation: Program 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.
authors.forename: Kevin P
authors.initials: KP
authors.lastname: White
authors.affiliation: Program 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.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ji
mesh_terms: D001499:Bayes Theorem; D030541:Databases, Genetic / Q000639:trends; D004843:Epistasis, Genetic; D023281:Genomics / Q000379:methods; D006801:Humans; D020407:Internet; D016013:Likelihood Functions; D009369:Neoplasms / Q000235:genetics*; D012984:Software; D014584:User-Computer Interface