AGENT for Exploring and Analyzing Gene Regulatory Networks from Arabidopsis

Vincent Lau & Nicholas J. Provart

Methods Mol Biol. 2023:2698:351-360. doi: 10.1007/978-1-0716-3354-0_20

Pubmed: 37682484


Gene regulatory networks (GRNs) are important for determining how an organism develops and how it responds to external stimuli. In the case of Arabidopsis thaliana, several GRNs have been identified covering many important biological processes. We present AGENT, the Arabidopsis GEne Network Tool, for exploring and analyzing published GRNs. Using tools in AGENT, regulatory motifs such as feed-forward loops can be easily identified. Nodes with high centrality-and hence importance-can likewise be identified. Gene expression data can also be overlaid onto GRNs to help discover subnetworks acting in specific tissues or under certain conditions.

Keywords: Bioinformatics; Feed-forward loops; Gene regulatory networks; Hypothesis generation; Motifs; Protein–DNA interactions; Protein–protein interactions.