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Mapping Mammalian 3D Genome Interactions with Micro-C-XL

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HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples.

Fritz Lekschas, Benjamin Bach, Peter Kerpedjiev

IEEE Transactions on Visualization and Computer Graphics

|September 4, 2017

Summary

HiPiler offers a novel interactive visualization for exploring large genome interaction matrices. This tool enhances the identification and analysis of regions of interest (ROIs) through snippet-based exploration.

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Area of Science:

Genomics
Bioinformatics
Data Visualization

Background:

Genome interaction matrices are crucial for understanding 3D genome structure but are often very large and sparse.
Existing visualization methods struggle with the effective exploration of specific regions of interest (ROIs) within these massive datasets.

Purpose of the Study:

To introduce HiPiler, an interactive visualization interface designed for the efficient exploration and analysis of ROIs in large genome interaction matrices.
To address the limitations of traditional matrix aggregation and pan-and-zoom techniques for ROI inspection and comparison.

Main Methods:

HiPiler treats ROIs as first-class objects, represented as interactive "snippets".
Utilizes scatterplots and dimension reduction for automatic layout and exploration of snippets.
Implements brushing and linking to connect snippets with the full genome interaction matrix.
Design informed by interviews with 10 domain experts in genome interaction matrix analysis.

Main Results:

HiPiler effectively supports six crucial exploration tasks identified for genome interaction matrix analysis.
User studies with domain experts demonstrated the usability of HiPiler.
The interface facilitated the discovery of new findings within the analyzed data.

Conclusions:

HiPiler provides a powerful and user-friendly solution for navigating and analyzing complex genome interaction data.
The snippet-based approach significantly improves the exploration of ROIs compared to traditional methods.
This visualization tool has the potential to advance genomic research by enabling deeper insights into genome organization.