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Technology Overview
OHSU # 2316 — A three-dimensional visualization system allowing simultaneous views of multivariate, time-series and network data
Summary:
It is often intractable to extract meaningful correlations and patterns from information-dense genome browser. This visualization tool enables multiple genes to be viewed in the same browser and allows greater efficiency when integrating a genome browser with a network visualizer.
Gene Models
● Using cylinders to model exon/intron regions
● Scaling genes to a 3D space
● Visualizing multiple genes in the same space
○ More efficient than reloading browser every time, as with 2D
○ Can view annotations of different genes simultaneously
Gene Annotations
● Use the outside of the exon/intron model to lay out tracks of annotation data
● Support for up to 8 tracks, currently 4 different track types
● Immediate track/gene and track/track comparisons
Networks
● Uses text in data files to show interactions between genes (e.g. from GeneMANIA interaction database (Wade-Farley et al. 2010)).
○ Physical Interaction, Co-expression, and Genetic interaction
● Genes are organized by certain characteristics, making it easier to see patterns/navigate
● Genes can be moved into different clusters
Future Features:
● Clustering for automatic layouts
● Arc tracks between different gene models to show long-range physical interactions
● Automatic loading of tracks from online gene browsers
● Ability to access external information about genes (e.g. links to web browsers)
● Virtual Reality Head-Mounted Display support
● Animated visualization of network structure changes
● Reference axes for clustering dimensions of genes in network
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