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Inferring Gene Regulatory Networks and Predicting the Effect of Gene Perturbations via IQCELL

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Embryo Models In Vitro

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2767))

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Abstract

IQCELL is a platform that infers Boolean gene regulatory networks from single-cell RNA sequencing data. Boolean networks can be simulated under normal and perturbed conditions. In this chapter, we provide a detailed guideline for implementing IQCELL from a raw dataset. The steps include processing data, inferring informative genes, inferring gene regulatory network, and simulating the resulted network under normal and perturbed conditions.

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Acknowledgments

Funding: TH and PWZ were supported by the Canadian Institutes of Health Research (CIHR), Foundation Grant FRN 154283, and the Natural Sciences and Engineering Research Council of Canada (NSERC), Discovery Grant RGPIN-2020-06496), to PWZ. PWZ is the Canada Research Chair in Stem Cell Bioengineering (https://www.chairs-chaires.gc.ca). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors declare that no competing interests exist.

Author information

Authors and Affiliations

  1. School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada

    Tiam Heydari & Peter W. Zandstra

  2. Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada

    Tiam Heydari & Peter W. Zandstra

Authors
  1. Tiam Heydari
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  2. Peter W. Zandstra
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Editor information

Editors and Affiliations

  1. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA

    Magdalena Zernicka-Goetz

  2. Ottawa, ON, Canada

    Kursad Turksen

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Heydari, T., Zandstra, P.W. (2023). Inferring Gene Regulatory Networks and Predicting the Effect of Gene Perturbations via IQCELL. In: Zernicka-Goetz, M., Turksen, K. (eds) Embryo Models In Vitro. Methods in Molecular Biology, vol 2767. Humana, New York, NY. https://doi.org/10.1007/7651_2022_465

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  • DOI: https://doi.org/10.1007/7651_2022_465

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3685-5

  • Online ISBN: 978-1-0716-3686-2

  • eBook Packages: Springer Protocols

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