title: Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome.
abstract: BACKGROUND
  New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation.
  
  
  RESULTS
  We have applied object-oriented technology to develop a downloadable visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome. In order to integrate and visualize large volume of data, novel statistical and mathematical approaches have been developed to reduce the size of the data. To our knowledge, this is the first such tool developed that can visualize human genome in three-dimension. We describe here the major features of Genome3D and discuss our multi-scale data framework using a representative basic physical model. We then demonstrate many of the issues and benefits of multi-resolution data integration.
  
  
  CONCLUSIONS
  Genome3D is a software visualization tool that explores a wide range of structural genomic and epigenetic data. Data from various sources of differing scales can be integrated within a hierarchical framework that is easily adapted to new developments concerning the structure of the physical genome. In addition, our tool has a simple annotation mechanism to incorporate non-structural information. Genome3D is unique is its ability to manipulate large amounts of multi-resolution data from diverse sources to uncover complex and new structural relationships within the genome.
authors.affiliation: Department of Biochemistry & Molecular Biology, Medical University of South Carolina, 135 Cannon Street, Suite 303E, Charleston, SC 29425, USA.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Asbury
authors.forename: Matt
authors.initials: M
authors.lastname: Mitman
authors.forename: Jijun
authors.initials: J
authors.lastname: Tang
authors.forename: W Jim
authors.initials: WJ
authors.lastname: Zheng
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D003628:Database Management Systems; D044127:Epigenesis, Genetic; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D021621:Imaging, Three-Dimensional; D008957:Models, Genetic; D008968:Molecular Conformation; D012984:Software; D014584:User-Computer Interface
references.citation: Radiat Environ Biophys. 2000 Jun;39(2):111-20
references.pmid: 10929379
references.citation: Chromosoma. 2006 Feb;115(1):1-14
references.pmid: 16362820
references.citation: Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):9021-5
references.pmid: 8415647
references.citation: Nucleic Acids Res. 1997 Sep 15;25(18):3733-42
references.pmid: 9278498
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D773-9
references.pmid: 18086701
references.citation: Proc Natl Acad Sci U S A. 1995 Mar 28;92(7):2710-4
references.pmid: 7708711
references.citation: Nature. 2000 Jan 6;403(6765):41-5
references.pmid: 10638745
references.citation: Structure. 2001 Feb 7;9(2):105-14
references.pmid: 11250195
references.citation: Science. 2002 Feb 15;295(5558):1306-11
references.pmid: 11847345
references.citation: Nat Genet. 2008 Feb;40(2):161-9
references.pmid: 18193043
references.citation: Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15632-7
references.pmid: 12438652
references.citation: Cell. 2002 Feb 22;108(4):475-87
references.pmid: 11909519
references.citation: Science. 2009 Oct 9;326(5950):289-93
references.pmid: 19815776
references.citation: Biophys J. 2007 Mar 1;92(5):1457-70
references.pmid: 17142268
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Mar;73(3 Pt 1):031919
references.pmid: 16605570
references.citation: Genome Res. 2007 Jun;17(6):691-707
references.pmid: 17567990
references.citation: Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7854-8
references.pmid: 8356094
references.citation: Cell. 2008 Mar 7;132(5):887-98
references.pmid: 18329373
references.citation: Nat Rev Genet. 2008 Mar;9(3):179-91
references.pmid: 18250624
references.citation: Science. 2008 Mar 28;319(5871):1793-4
references.pmid: 18369139
references.citation: Cell. 2006 Jan 13;124(1):207-19
references.pmid: 16413492
references.citation: Nature. 1997 Sep 18;389(6648):251-60
references.pmid: 9305837
references.citation: Science. 2004 Oct 22;306(5696):636-40
references.pmid: 15499007
references.citation: Bioinformatics. 2005 May 15;21(10):2502-9
references.pmid: 15731211