Key transcription factors (TFs) controlling the morphogenesis of flowers and leaves have been identified in the model plant Arabidopsis thaliana. Recent genome-wide approaches based on chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) enable systematic identification of genome-wide TF binding sites (TFBSs) of these regulators. Here, we describe a computational pipeline for analyzing ChIP-seq data to identify TFBSs and to characterize gene regulatory networks (GRNs) with applications to the regulatory studies of flower development. In particular, we provide step-by-step instructions on how to download, analyze, visualize, and integrate genome-wide data in order to construct GRNs for beginners of bioinformatics. The practical guide presented here is ready to apply to other similar ChIP-seq datasets to characterize GRNs of interest.
CITATION STYLE
Chen, D., & Kaufmann, K. (2017). Integration of genome-wide TF binding and gene expression data to characterize gene regulatory networks in plant development. In Methods in Molecular Biology (Vol. 1629, pp. 239–269). Humana Press Inc. https://doi.org/10.1007/978-1-4939-7125-1_16
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