Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome.
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.
Asbury
Thomas M
TM
Department of Biochemistry & Molecular Biology, Medical University of South Carolina, 135 Cannon Street, Suite 303E, Charleston, SC 29425, USA.
Mitman
Matt
M
Tang
Jijun
J
Zheng
W Jim
WJ
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
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