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Bioinformatic Tools in Arabidopsis Research

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Arabidopsis Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2200))

Abstract

Bioinformatic tools are now an everyday part of a plant researcher’s collection of protocols. They allow almost instantaneous access to large data sets encompassing genomes, transcriptomes, proteomes, epigenomes, and other “-omes,” which are now being generated with increasing speed and decreasing cost. With the appropriate queries, such tools can generate quality hypotheses, sometimes without the need for new experimental data. In this chapter, we will investigate some of the tools used for examining gene expression and coexpression patterns, performing promoter analyses and functional classification enrichment for sets of genes, and exploring protein–protein and protein–DNA interactions in Arabidopsis. We will also cover additional tools that allow integration of data from several sources for improved hypothesis generation.

G. Alex Mason and Alex Cantó-Pastor are co-first authors.

This chapter is a revision of a chapter with the same name by Miguel de Lucas, Nicholas J. Provart, and Siobhan Brady in Arabidopsis Protocols (2014, 1062, pp 97–136), edited by José Juan Sanchez Serrano. All material has been revised and updated as of May 2019, and several new tools are described.

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Authors and Affiliations

  1. Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA

    G. Alex Mason, Alex Cantó-Pastor & Siobhan M. Brady

  2. Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada

    Nicholas J. Provart

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  1. G. Alex Mason
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  2. Alex Cantó-Pastor
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  3. Siobhan M. Brady
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  4. Nicholas J. Provart
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Corresponding author

Correspondence to Nicholas J. Provart .

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Editors and Affiliations

  1. Centro Nacional de Biotecnología, CSIC Centro Nacional de Biotecnología, Madrid, Spain

    Jose J. Sanchez-Serrano

  2. Centro de Investigaciones Biologicas, CSIC Madrid Centro de Investigaciones Biologicas, Madrid, Spain

    Julio Salinas

1 Electronic Supplementary Material

Table S1

ABI3 developmentally coexpressed genes (DOCX 28 kb)

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Alex Mason, G., Cantó-Pastor, A., Brady, S.M., Provart, N.J. (2021). Bioinformatic Tools in Arabidopsis Research. In: Sanchez-Serrano, J.J., Salinas, J. (eds) Arabidopsis Protocols . Methods in Molecular Biology, vol 2200. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0880-7_2

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