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Dimensionality reduction by UMAP to visualize physical and genetic interactions

Author

Listed:
  • Michael W. Dorrity

    (University of Washington)

  • Lauren M. Saunders

    (University of Washington)

  • Christine Queitsch

    (University of Washington)

  • Stanley Fields

    (University of Washington
    University of Washington)

  • Cole Trapnell

    (University of Washington)

Abstract

Dimensionality reduction is often used to visualize complex expression profiling data. Here, we use the Uniform Manifold Approximation and Projection (UMAP) method on published transcript profiles of 1484 single gene deletions of Saccharomyces cerevisiae. Proximity in low-dimensional UMAP space identifies groups of genes that correspond to protein complexes and pathways, and finds novel protein interactions, even within well-characterized complexes. This approach is more sensitive than previous methods and should be broadly useful as additional transcriptome datasets become available for other organisms.

Suggested Citation

  • Michael W. Dorrity & Lauren M. Saunders & Christine Queitsch & Stanley Fields & Cole Trapnell, 2020. "Dimensionality reduction by UMAP to visualize physical and genetic interactions," Nature Communications, Nature, vol. 11(1), pages 1-6, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15351-4
    DOI: 10.1038/s41467-020-15351-4
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    Cited by:

    1. Huanhuan Tan & Weixu Wang & Congjin Zhou & Yanfeng Wang & Shu Zhang & Pinglan Yang & Rui Guo & Wei Chen & Jinwen Zhang & Lan Ye & Yiqiang Cui & Ting Ni & Ke Zheng, 2023. "Single-cell RNA-seq uncovers dynamic processes orchestrated by RNA-binding protein DDX43 in chromatin remodeling during spermiogenesis," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    2. Max Lam & Chia-Yen Chen & W. David Hill & Charley Xia & Ruoyu Tian & Daniel F. Levey & Joel Gelernter & Murray B. Stein & Alexander S. Hatoum & Hailiang Huang & Anil K. Malhotra & Heiko Runz & Tian Ge, 2022. "Collective genomic segments with differential pleiotropic patterns between cognitive dimensions and psychopathology," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    3. Kristina M. Garske & Asha Kar & Caroline Comenho & Brunilda Balliu & David Z. Pan & Yash V. Bhagat & Gregory Rosenberg & Amogha Koka & Sankha Subhra Das & Zong Miao & Janet S. Sinsheimer & Jaakko Kapr, 2023. "Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Erik Hermansen & David A. Klindt & Benjamin A. Dunn, 2024. "Uncovering 2-D toroidal representations in grid cell ensemble activity during 1-D behavior," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

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