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Methods Mol Biol. 2014;1062:97-136. doi: 10.1007/978-1-62703-580-4_5.

Bioinformatic tools in Arabidopsis research.

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


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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