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Arabidopsis Protocols pp 97–136Cite as

Bioinformatic Tools in Arabidopsis Research

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1062))

Abstract

Bioinformatic tools are an increasingly important resource for Arabidopsis researchers. With them, it is possible to rapidly query the large data sets covering genomes, transcriptomes, proteomes, epigenomes, and other “omes” that have been generated in the past decade. Often these tools can be used to generate quality hypotheses at the click of a mouse. In this chapter, we cover the use of bioinformatic tools for examining gene expression and coexpression patterns, performing promoter analyses, looking for functional classification enrichment for sets of genes, and investigating protein–protein interactions. We also introduce bioinformatic tools that allow integration of data from several sources for improved hypothesis generation.

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Author information

Authors and Affiliations

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

    Miguel de Lucas & Siobhan M. Brady

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

    Nicholas J. Provart

Authors
  1. Miguel de Lucas
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  2. Nicholas J. Provart
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  3. Siobhan M. Brady
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Editor information

Editors and Affiliations

  1. CSIC Centro Nacional de Biotecnología, Madrid, Spain

    Jose J. Sanchez-Serrano

  2. Depto. Biologia de Plantas, CSIC Madrid Centro de Investigaciones Biologicas, Madrid, Spain

    Julio Salinas

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de Lucas, M., Provart, N.J., Brady, S.M. (2014). Bioinformatic Tools in Arabidopsis Research. In: Sanchez-Serrano, J., Salinas, J. (eds) Arabidopsis Protocols. Methods in Molecular Biology, vol 1062. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-580-4_5

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  • DOI: https://doi.org/10.1007/978-1-62703-580-4_5

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-579-8

  • Online ISBN: 978-1-62703-580-4

  • eBook Packages: Springer Protocols

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