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A Flexible Protocol for Targeted Gene Co-expression Network Analysis

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Plant Isoprenoids

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1153))

Abstract

The inference of gene co-expression networks is a valuable resource for novel hypotheses in experimental research. Routine high-throughput microarray transcript profiling experiments and the rapid development of next-generation sequencing (NGS) technologies generate a large amount of publicly available data, enabling in silico reconstruction of regulatory networks. Analysis of the transcriptome under various experimental conditions proved that genes with an overall similar expression pattern often have similar functions. Consistently, genes involved in the same metabolic pathway are found in co-expressed modules. In this chapter, we describe a detailed workflow for analyzing gene co-expression networks using large-scale gene expression data and explain critical steps from design and data analysis to prediction of functionally related modules. This protocol is platform independent and can be used for data generated by ATH1 arrays, tiling arrays, or RNA sequencing for any organism. The most important feature of this workflow is that it can infer statistically significant gene co-expression networks for any number of genes and transcriptome data sets and it does not involve any particular hardware requirements.

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Acknowledgments

We thank Dr. Eva Vranová and Prof. Peter Bühlmann for helpful discussions and Philipp Ihmor for critically reading the manuscript. This work was supported by the Seventh Framework Program of the European Commission through the TiMet collaborative project (grant 245143) to W.G.

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Authors and Affiliations

  1. Department of Biology, Plant Biotechnology, ETH Zurich, Universitätstrasse 2, 8092, Zurich, Switzerland

    Diana Coman & Wilhelm Gruissem

  2. Seminar for Statistics, ETH Zurich, Zurich, Switzerland

    Philipp Rütimann

  3. Functional Genomics Center Zurich, ETH Zurich, Zurich, Switzerland

    Wilhelm Gruissem

Authors
  1. Diana Coman
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  2. Philipp Rütimann
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  3. Wilhelm Gruissem
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Corresponding author

Correspondence to Wilhelm Gruissem .

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Editors and Affiliations

  1. Centre for Research in Agricultural Genomic (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain

    Manuel Rodríguez-Concepción

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Coman, D., Rütimann, P., Gruissem, W. (2014). A Flexible Protocol for Targeted Gene Co-expression Network Analysis. In: Rodríguez-Concepción, M. (eds) Plant Isoprenoids. Methods in Molecular Biology, vol 1153. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0606-2_21

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  • DOI: https://doi.org/10.1007/978-1-4939-0606-2_21

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0605-5

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