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Technology Overview

OHSU # 2316 — A three-dimensional visualization system allowing simultaneous views of multivariate, time-series and network data



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


● 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