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Methods Mol Biol. 2017;1533:119-148.

The Bio-Analytic Resource for Plant Biology.

Author information

1
Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada.
2
Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada. nicholas.provart@utoronto.ca.

Abstract

Bioinformatic tools have become part of the way plant researchers undertake investigations. Large data sets encompassing genomes, transcriptomes, proteomes, epigenomes, and other "-omes" that have been generated in the past decade may be easily accessed with such tools, such that hypotheses may be generated at the click of a mouse. In this chapter, we'll cover the use of bioinformatic tools available at the Bio-Analytic Resource for Plant Biology at http://bar.utoronto.ca for exploring gene expression and coexpression patterns, undertaking promoter analyses, performing functional classification enrichment analyses for sets of genes, and examining protein-protein interactions. We also touch on some newer bioinformatic tools that allow integration of data from several sources for improved hypothesis generation, both for Arabidopsis and translationally. Most of the data sets come from Arabidopsis, but useful BAR tools for other species will be mentioned where appropriate.

KEYWORDS:

Bioinformatics; Coexpression; Functional classification; Functional genomics; Hypothesis generation; In silico; Promoter analysis; Protein-protein interactions; Proteomics; Subcellular localization; Transcriptomics; Translational biology; eFP

PMID:
27987167
DOI:
10.1007/978-1-4939-6658-5_6
[Indexed for MEDLINE]

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