Abstract
The inference of gene regulatory networks can reveal molecular connections underlying biological processes and improve our understanding of complex biological phenomena in plants. Many previous network studies have inferred networks using only one type of omics data, such as transcriptomics. However, given more recent work applying multi-omics integration in plant biology, such as combining (phospho)proteomics with transcriptomics, it may be advantageous to integrate multiple omics data types into a comprehensive network prediction. Here, we describe a state-of-the-art approach for integrating multi-omics data with gene regulatory network inference to describe signaling pathways and uncover novel regulators. We detail how to download and process transcriptomics and (phospho)proteomics data for network inference, using an example dataset from the plant hormone signaling field. We provide a step-by-step protocol for inference, visualization, and analysis of an integrative multi-omics network using currently available methods. This chapter serves as an accessible guide for novice and intermediate bioinformaticians to analyze their own datasets and reanalyze published work.
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Acknowledgments
This work was supported by a USDA NIFA AFRI grant to DRK and JWW (Award No. 2020-67013-30914) and Hatch Act and State of Iowa funds to DRK (Project No. IOW03649) and JWW (Project No. IOW04308). DRK is also supported by NSF Award 2118253. Work in JWW’s laboratory is supported by the Iowa State University Plant Science Institute, NIH (GM120316), and NSF (2039489, 2040582, 1759023 & 1818160). Work in MGL’s lab is funded by the Australian Research Council (ARC) Industrial Transformation Hub in Medicinal Agriculture (IH180100006) with institutional and industry partners and by ARC Discovery Program grant DP220102840. Figures were created with Biorender.com.
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Clark, N.M., Hurgobin, B., Kelley, D.R., Lewsey, M.G., Walley, J.W. (2023). A Practical Guide to Inferring Multi-Omics Networks in Plant Systems. In: Kaufmann, K., Vandepoele, K. (eds) Plant Gene Regulatory Networks. Methods in Molecular Biology, vol 2698. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3354-0_15
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DOI: https://doi.org/10.1007/978-1-0716-3354-0_15
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