Difference between revisions of "3D Chromosome Viewer"

Revision as of 13:01, 1 June 2012

Background and Project Overview

Most genome browsers display DNA linearly, using single-dimensional depictions that are useful to examine certain epigenetic mechanisms such as DNA methylation. However, these representations are insufficient to visualize intra-chromosomal interactions and relationships between distal genome features. Relationships between DNA regions may be difficult to decipher or missed entirely if those regions are distant in one dimension but could be spatially proximal when mapped to three-dimensional space. For example, the visualization of enhancers folding over genes is only fully expressed in three-dimensional space. Thus, to accurately understand DNA behavior during gene expression, a means to model chromosomes is essential. The purpose of this project is to facilitate three-dimensional chromosome modelling.

The three-dimensional chromosome model will contain a three-tier model of visualization where each subsequent tier is a greater detailed segment of the preceding tier. At the highest level, the first tier models entire chromosomes consisting of interconnected cylinders. Each cylinder in the first tier represents a chromosomal domain that links to the second tier of visualization. At the next level, the second tier models chromosome domains consisting of cylinders representing bins of 20,000 and 40,000 base pairs. The second tier also depicts genomic features--such as genes, enhancers, and CTCF binding sites-- with different color schemes that elucidate interactions between regions. Each cylinder in the second tier links to the third and final tier, which is a genome browser displaying a detailed linear annotation of the corresponding bin. As a stretch goal, the third tier could also render a helix structure of color-coded base pairs.

The potential applications of this project include the visualization of intra-chromosomal interactions, genomic features and their relationships, and the discovery of new genes.

Status

• Loaded world and menu for initial set up of view
• Added functionality to parse data files to extract data needed for rendering
• Rendered spheres at x,y,z coordinates specified in data files
• Created mathematically manipulated cylinders to connect spheres to create a contiguous structure
• Added options to render any of 23 chromosomes from the menu
• Added colour to differentiate between loose, condensed, and intermediate areas of the chromosome
• Added clear all button

To-Do

• Add functionality to render any chromosome/data file
• Implement transition to second tier functionality
  • Display domain of chromosome bin on click
  • Add animation
• Add colour scheme to differentiate different points of interest on specific chromosomes
• Add labels
• Convert so SceneObject for rendering of multiple chromosomes on the same scene
• Auto adjust camera upon loading of new chromosome

Future Work

• Add interactivity
• Implement the next two tiers of the three-tier model described in the Project Overview
• Add functionality for scripting support
• Add support for rendering description files dynamically
• Extend models to websites and/or smart phones

Participants

Software Developers:

• Yixin Zhu

Project Advisors:

• Jurgen Schulze

Misc. Development Assistance:

• Philip Weber
• Andrew Prudhomme
• Alfred Tarng