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PhosPhAt 4.0: An Updated Arabidopsis Database for Searching Phosphorylation Sites and Kinase-Target Interactions

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Plant Phosphoproteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2358))

Abstract

The PhosPhAt 4.0 database contains information on Arabidopsis phosphorylation sites identified by mass spectrometry in large-scale experiments from different research groups. So far PhosPhAt 4.0 has been one of the most significant large-scale data resources for plant phosphorylation studies. Functionalities of the web application, besides display of phosphorylation sites, include phosphorylation site prediction and kinase–target relationships retrieval. Here, we present an overview and user instructions for the PhosPhAt 4.0 database, with strong emphasis on recent renewals regarding protein annotation by SUBA4.0 and Mapman4, and additional phosphorylation site information imported from other databases, such as UniProt. Here, we provide a user guide for the retrieval of phosphorylation motifs from the kinase–target database and how to visualize these results. The improvements incorporated into the PhosPhAt 4.0 database have produced much more functionality and user flexibility for phosphoproteomic analysis.

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Authors and Affiliations

  1. Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany

    Lin Xi, Zhaoxia Zhang & Waltraud X. Schulze

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  1. Lin Xi
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  2. Zhaoxia Zhang
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  3. Waltraud X. Schulze
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Correspondence to Lin Xi .

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Editors and Affiliations

  1. State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China

    Xu Na Wu

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Xi, L., Zhang, Z., Schulze, W.X. (2021). PhosPhAt 4.0: An Updated Arabidopsis Database for Searching Phosphorylation Sites and Kinase-Target Interactions. In: Wu, X.N. (eds) Plant Phosphoproteomics. Methods in Molecular Biology, vol 2358. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1625-3_14

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  • DOI: https://doi.org/10.1007/978-1-0716-1625-3_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1624-6

  • Online ISBN: 978-1-0716-1625-3

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