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Connecting omics signatures and revealing biological mechanisms with iLINCS

Author

Listed:
  • Marcin Pilarczyk

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Mehdi Fazel-Najafabadi

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Michal Kouril

    (LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    Cincinnati Children’s Hospital Medical Center)

  • Behrouz Shamsaei

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Juozas Vasiliauskas

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Wen Niu

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Naim Mahi

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Lixia Zhang

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Nicholas A. Clark

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Yan Ren

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Shana White

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Rashid Karim

    (University of Cincinnati
    University of Cincinnati)

  • Huan Xu

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Jacek Biesiada

    (University of Cincinnati)

  • Mark F. Bennett

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Sarah E. Davidson

    (University of Cincinnati)

  • John F. Reichard

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Kurt Roberts

    (University of Cincinnati)

  • Vasileios Stathias

    (LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    University of Miami)

  • Amar Koleti

    (LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    University of Miami)

  • Dusica Vidovic

    (LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    University of Miami)

  • Daniel J. B. Clarke

    (LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    Icahn School of Medicine at Mount Sinai)

  • Stephan C. Schürer

    (LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    University of Miami)

  • Avi Ma’ayan

    (LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    Icahn School of Medicine at Mount Sinai)

  • Jarek Meller

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

  • Mario Medvedovic

    (University of Cincinnati
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC)
    LINCS Data Coordination and Integration Center (DCIC))

Abstract

There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses and visualization that do not require programming skills. Here we present iLINCS ( http://ilincs.org ), an integrative web-based platform for analysis of omics data and signatures of cellular perturbations. The platform facilitates mining and re-analysis of the large collection of omics datasets (>34,000), pre-computed signatures (>200,000), and their connections, as well as the analysis of user-submitted omics signatures of diseases and cellular perturbations. iLINCS analysis workflows integrate vast omics data resources and a range of analytics and interactive visualization tools into a comprehensive platform for analysis of omics signatures. iLINCS user-friendly interfaces enable execution of sophisticated analyses of omics signatures, mechanism of action analysis, and signature-driven drug repositioning. We illustrate the utility of iLINCS with three use cases involving analysis of cancer proteogenomic signatures, COVID 19 transcriptomic signatures and mTOR signaling.

Suggested Citation

  • Marcin Pilarczyk & Mehdi Fazel-Najafabadi & Michal Kouril & Behrouz Shamsaei & Juozas Vasiliauskas & Wen Niu & Naim Mahi & Lixia Zhang & Nicholas A. Clark & Yan Ren & Shana White & Rashid Karim & Huan, 2022. "Connecting omics signatures and revealing biological mechanisms with iLINCS," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32205-3
    DOI: 10.1038/s41467-022-32205-3
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    References listed on IDEAS

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    1. Charles M. Perou & Therese Sørlie & Michael B. Eisen & Matt van de Rijn & Stefanie S. Jeffrey & Christian A. Rees & Jonathan R. Pollack & Douglas T. Ross & Hilde Johnsen & Lars A. Akslen & Øystein Flu, 2000. "Molecular portraits of human breast tumours," Nature, Nature, vol. 406(6797), pages 747-752, August.
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    1. Matteo Marchesini & Andrea Gherli & Elisa Simoncini & Lucas Moron Dalla Tor & Anna Montanaro & Natthakan Thongon & Federica Vento & Chiara Liverani & Elisa Cerretani & Anna D’Antuono & Luca Pagliaro &, 2024. "Orthogonal proteogenomic analysis identifies the druggable PA2G4-MYC axis in 3q26 AML," Nature Communications, Nature, vol. 15(1), pages 1-22, December.

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