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Feature-Centric Visual Exploration of Genome Interaction Maps

Feature-Centric Visual Exploration of Genome Interaction Maps

Venue: ISMB 2018 in Chicago
Session: BioVis

Fritz Lekschas

July 09, 2018
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  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
    [email protected]
    @flekschas
    lekschas.de
    POSTER: B-765

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