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AthaMap Web Tools for the Analysis of Transcriptional and Posttranscriptional Regulation of Gene Expression in Arabidopsis thaliana

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Plant Circadian Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1158))

Abstract

The AthaMap database provides a map of verified and predicted transcription factor (TF) and small RNA-binding sites for the A. thaliana genome. The database can be used for bioinformatic predictions of putative regulatory sites. Several online web tools are available that address specific questions. Starting with the identification of transcription factor-binding sites (TFBS) in any gene of interest, colocalizing TFBS can be identified as well as common TFBS in a set of user-provided genes. Furthermore, genes can be identified that are potentially targeted by specific transcription factors or small inhibitory RNAs. This chapter provides detailed information on how each AthaMap web tool can be used online. Examples on how this database is used to address questions in circadian and diurnal regulation are given. Furthermore, complementary databases and databases that go beyond questions addressed with AthaMap are discussed.

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Acknowledgements

The work on the AthaMap database was supported by grants from the German Federal Ministry for Education and Research (BMBF). We would like to thank Martin Schindler, Nils Ole Steffens, Claudia Galuschka, Yuri Brill, Julio C. Bolívar, Jonas Ruhe, and Stefan Engelmann for their work on the AthaMap database and web tools. Currently, AthaMap is being curated by Artyom Romanov. We also want to thank Edgar Wingender for stimulating our interest in bioinformatics.

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  1. Institut für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany

    Reinhard Hehl & Lorenz Bülow

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  1. Reinhard Hehl
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  2. Lorenz Bülow
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Correspondence to Reinhard Hehl .

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  1. Molecular Cell Physiology, University of Bielefeld, Germany

    Dorothee Staiger

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Hehl, R., Bülow, L. (2014). AthaMap Web Tools for the Analysis of Transcriptional and Posttranscriptional Regulation of Gene Expression in Arabidopsis thaliana . In: Staiger, D. (eds) Plant Circadian Networks. Methods in Molecular Biology, vol 1158. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0700-7_9

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  • DOI: https://doi.org/10.1007/978-1-4939-0700-7_9

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