Abstract
BackgroundNew 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.ResultsWe 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.ConclusionsGenome3D 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.
Highlights
New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear
Genome3D allows the user to specify the degree of detail to view, and the corresponding data is loaded dynamically
To illustrate the capability of Genome3D to integrate and examine data of appropriate scales, we constructed an elementary model of the physical genome
Summary
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. Genome-wide epigenetic characteristics such as DNA and histone modifications, nucleosome distributions, along with transcriptional and replication center structural insights are rapidly changing the way the genome is understood These new data from high-throughput sources are often demonstrating that much of the genome’s functional landscape resides in extra-sequential properties. With this influx of new detail about the higher-level structure and dynamics of the genome, new techniques will be required to visualize and model the full extent of genomic interactions and function. In spite of the many recent efforts to measure and model the genome structure at various resolutions and detail [3,4,5,6,7,8,9,10], little work has focused on combining these models into a plausible aggregate, or has taken advantage of the large amount of genomic and epigenomic data available from new high-throughput approaches
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