Feature-Centric Visual Exploration of Genome Interaction Maps

Venue: ISMB 2018 in Chicago
Session: BioVis

Transcript

1. Feature-Centric Visual
   Exploration of Genome
   Interaction Maps
   Fritz Lekschas, PhD candidate

   Harvard University
   Benjamin Bach, Peter Kerpedjiev, Michael Behrisch, Nils Gehlenborg,
   and Hanspeter Pfister
   July 9th, 2018
   ISMB 2018
   

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2. Cell Nucleus Contact Sequencing Heatmap
   3D GENOME
   

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3. Gene regulation:
   Enhancer-promoter
   Structural variation:
   Break points
   Cell dynamics:
   Differentiation
   Cell cycle
   WHY CARE?
   

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4. 3 million × 3 million
   

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5. PATTERNS
   

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6. CHALLENGES
   • Size of the heatmap
   • Many called features
   • No ground truth
   GOALS
   • Quality control
   • Pattern discovery
   • Pattern correlation
   CHALLENGES
   

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12. Efficiency
    Show all insets

    Close to origin
    Minimize occlusion
    Show all insets
    

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13. Efficiency
    Show all insets

    Close to origin
    Minimize occlusion
    Close to origin
    

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14. Efficiency
    Show all insets

    Close to origin
    Minimize occlusion
    Minimize occlusion
    

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16. Performance comparison in pattern search on images and
    genome interaction maps
    User study: 18 participants and 6 domain experts
    Techniques:
    Results: faster pattern search

    more accurate pattern comparison

    easy-to-learn & easy-to-use
    EVALUATION
    

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17. CONCLUSION
    Explore local features in
    spatial context
    Faster pattern search
    Improved navigation
    

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18. Thank You!
    MORE INFORMATION
    scalable-insets.lekschas.de
    SOURCE CODE
    github.com/flekschas/higlass-scalable-insets
    CONTACT
    lekschas@seas.harvard.edu
    @flekschas
    lekschas.de
    POSTER: B-765
    

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