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Proceedings Paper

3D chromosome rendering from Hi-C data using virtual reality
Author(s): Yixin Zhu; Siddarth Selvaraj; Philip Weber; Jennifer Fang; Jürgen P. Schulze; Bing Ren
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Paper Abstract

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 intrachromosomal 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. Using coordinates generated from Hi-C interaction frequency data, we have created interactive 3D models of whole chromosome structures and its respective domains. We have also rendered information on genomic features such as genes, CTCF binding sites, and enhancers. The goal of this article is to present the procedure, findings, and conclusions of our models and renderings.

Paper Details

Date Published: 8 February 2015
PDF: 8 pages
Proc. SPIE 9397, Visualization and Data Analysis 2015, 93970Q (8 February 2015); doi: 10.1117/12.2083470
Show Author Affiliations
Yixin Zhu, Univ. of California, San Diego (United States)
Siddarth Selvaraj, Univ. of California, San Diego (United States)
Philip Weber, Univ. of California, San Diego (United States)
Jennifer Fang, Univ. of California, San Diego (United States)
Jürgen P. Schulze, Univ. of California, San Diego (United States)
Bing Ren, Univ. of California, San Diego (United States)

Published in SPIE Proceedings Vol. 9397:
Visualization and Data Analysis 2015
David L. Kao; Ming C. Hao; Mark A. Livingston; Thomas Wischgoll, Editor(s)

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