Abstract
Reconstruction of gene regulatory networks is a very important but difficult issue in plant sciences. Recently, numerous high-throughput techniques, such as chromatin immunoprecipitation sequencing (ChIP-seq) and DNA affinity purification sequencing (DAP-seq), have been developed to identify the genomic binding landscapes of regulatory factors. To understand the relationships among transcription factors (TFs) and their corresponding binding sites on target genes is usually the first step for elucidating gene regulatory mechanisms. Therefore, a good database for plant TFs and transcription factor binding sites (TFBSs) will be useful for starting a series of complex experiments. In this chapter, PlantPAN (version 3.0) is utilized as an example to explain how bioinformatics systems advance research on gene regulation.
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Acknowledgments
The authors would like to thank the Ministry of Science and Technology (MOST 108-2311-B-006 -002 -MY3 and MOST 110-2918-I-006-001) of the Republic of China for financially supporting this research. Computational analyses, data mining, and storage were performed using the system provided by the Bioinformatics Core at the National Cheng Kung University and National Center for High-performance Computing (NCHC) of the National Applied Research Laboratories (NARLabs), supported by the Ministry of Science and Technology, Taiwan.
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Chang, WC., Chow, CN. (2023). Database for Plant Transcription Factor Binding Sites. In: Song, Q., Tao, Z. (eds) Transcription Factor Regulatory Networks. Methods in Molecular Biology, vol 2594. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2815-7_13
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DOI: https://doi.org/10.1007/978-1-0716-2815-7_13
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