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Inferring Gene Regulatory Networks from Multiple Datasets

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Gene Regulatory Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1883))

Abstract

Gaussian process dynamical systems (GPDS) represent Bayesian nonparametric approaches to inference of nonlinear dynamical systems, and provide a principled framework for the learning of biological networks from multiple perturbed time series measurements of gene or protein expression. Such approaches are able to capture the full richness of complex ODE models, and can be scaled for inference in moderately large systems containing hundreds of genes. Related hierarchical approaches allow for inference from multiple datasets in which the underlying generative networks are assumed to have been rewired, either by context-dependent changes in network structure, evolutionary processes, or synthetic manipulation. These approaches can also be used to leverage experimentally determined network structures from one species into another where the network structure is unknown. Collectively, these methods provide a comprehensive and flexible platform for inference from a diverse range of data, with applications in systems and synthetic biology, as well as spatiotemporal modelling of embryo development. In this chapter we provide an overview of GPDS approaches and highlight their applications in the biological sciences, with accompanying tutorials available as a Jupyter notebook from https://github.com/cap76/GPDS.

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Acknowledgements

CAP is supported by the Wellcome Trust (grant 083089/Z/07/Z). IG is supported by EPSRC/BBSRC research grant EP/L016494/1. AS is supported by a 4-year Wellcome Trust PhD Scholarship and Cambridge International Trust Scholarship. DLW acknowledges support from the Engineering and Physical Science Research Council (grant EP/R014337/1).

CAP, IG, and AS BBSRC-EPSRC funded OpenPlant Synthetic Biology Research Centre (BB/L014130/1) through the OpenPlant Fund scheme. CAP and AS also thank M. Azim Surani for his support.

Author information

Authors and Affiliations

  1. Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK

    Christopher A. Penfold & Anastasiya Sybirna

  2. Warwick Integrative Synthetic Biology Centre, School of Engineering, University of Warwick, Coventry, UK

    Iulia Gherman

  3. Wellcome/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK

    Anastasiya Sybirna

  4. Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge, UK

    Anastasiya Sybirna

  5. Department of Statistics and Systems Biology Centre, University of Warwick, Coventry, UK

    David L. Wild

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  1. Christopher A. Penfold
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  2. Iulia Gherman
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  3. Anastasiya Sybirna
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  4. David L. Wild
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Corresponding author

Correspondence to Christopher A. Penfold .

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Editors and Affiliations

  1. School of Informatics, University of Edinburgh, Edinburgh, UK

    Guido Sanguinetti

  2. Department of Electrical Engineering and Computer Science, University of Liège, Liège, Belgium

    Vân Anh Huynh-Thu

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Penfold, C.A., Gherman, I., Sybirna, A., Wild, D.L. (2019). Inferring Gene Regulatory Networks from Multiple Datasets. In: Sanguinetti, G., Huynh-Thu, V. (eds) Gene Regulatory Networks. Methods in Molecular Biology, vol 1883. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8882-2_11

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  • DOI: https://doi.org/10.1007/978-1-4939-8882-2_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8881-5

  • Online ISBN: 978-1-4939-8882-2

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