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FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces

AuthorsContreras-Moreira, Bruno CSIC ORCID ; Sebastián Yagüe, Álvaro CSIC
transcription factor
DNA binding
DNA motif
protein domain
Issue DateAug-2016
CitationContreras-Moreira B, Sebastián A. FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces. In: Hehl R (ed.), Plant Synthetic Promoters (Methods in Molecular Biology 1482: 259-277), New York, Springer Science+Business Media. DOI: 10.1007/978-1-4939-6396-6_17 (2016)
AbstractFootprintDB is a database and search engine that compiles regulatory sequences from open access libraries of curated DNA cis-elements and motifs, and their associated transcription factors (TFs). It systematically annotates the binding interfaces of the TFs by exploiting protein-DNA complexes deposited in the Protein Data Bank. Each entry in footprintDB is thus a DNA motif linked to the protein sequence of the TF(s) known to recognize it, and in most cases, the set of predicted interface residues involved in specific recognition. This chapter explains step-by-step how to search for DNA motifs and protein sequences in footprintDB and how to focus the search to a particular organism. Two real-world examples are shown where this software was used to analyze transcriptional regulation in plants. Results are described with the aim of guiding users on their interpretation, and special attention is given to the choices users might face when performing similar analyzes.
Description28 Pags.- 8 Figs. The definitive version is available at: http://link.springer.com/bookseries/7651 and http://link.springer.com/book/10.1007/978-1-4939-6396-6.
Publisher version (URL)http://dx.doi.org/10.1007/978-1-4939-6396-6_17
ISBN978-1-4939-6394-2 (Print)
ISSNISBN 978-1-4939-6396-6 (Online)
Appears in Collections:(EEAD) Libros y partes de libros
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