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Root Development pp 275–301Cite as

Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1761))

Abstract

The rapid increase in the availability of transcriptomics data generated by RNA sequencing represents both a challenge and an opportunity for biologists without bioinformatics training. The challenge is handling, integrating, and interpreting these data sets. The opportunity is to use this information to generate testable hypothesis to understand molecular mechanisms controlling gene expression and biological processes (Fig. 1). A successful strategy to generate tractable hypotheses from transcriptomics data has been to build undirected network graphs based on patterns of gene co-expression. Many examples of new hypothesis derived from network analyses can be found in the literature, spanning different organisms including plants and specific fields such as root developmental biology.

In order to make the process of constructing a gene co-expression network more accessible to biologists, here we provide step-by-step instructions using published RNA-seq experimental data obtained from a public database. Similar strategies have been used in previous studies to advance root developmental biology. This guide includes basic instructions for the operation of widely used open source platforms such as Bio-Linux, R, and Cytoscape. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be easily adapted to work with RNA-seq data from any organism.

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Acknowledgments

Research in our group is funded by Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), MIISSB Iniciativa Científica Milenio-MINECON, Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1141097, and EvoNet (DE-SC0014377).

Author information

Author notes

  1. Orlando Contreras-López and Tomás C. Moyano contributed equally to this work.

Authors and Affiliations

  1. Departamento de Genética Molecular y Microbiología, FONDAP Center for Genome Regulation, Millennium Institute for Integrative Systems and Synthetic Biology (MIISSB), Pontificia Universidad Católica de Chile, Santiago, Chile

    Orlando Contreras-López, Tomás C. Moyano, Daniela C. Soto & Rodrigo A. Gutiérrez

Authors
  1. Orlando Contreras-López
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  2. Tomás C. Moyano
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  3. Daniela C. Soto
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  4. Rodrigo A. Gutiérrez
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Corresponding author

Correspondence to Rodrigo A. Gutiérrez .

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Editors and Affiliations

  1. Gregor Mendel Institute of Molecular Plant Biology, Vienna, Wien, Austria

    Daniela Ristova

  2. Institute of Applied Genetics & Cell Biology, University of Natural Resources and Life Sciences, Vienna, Wien, Austria

    Elke Barbez

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Contreras-López, O., Moyano, T.C., Soto, D.C., Gutiérrez, R.A. (2018). Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data. In: Ristova, D., Barbez, E. (eds) Root Development. Methods in Molecular Biology, vol 1761. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7747-5_21

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  • DOI: https://doi.org/10.1007/978-1-4939-7747-5_21

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  • Publisher Name: Humana Press, New York, NY

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