Abstract
Plant sumoylation research has seen significant advances in recent years, particularly since high-throughput proteomics strategies have enabled the discovery of hundreds of potential SUMO targets and interactors of SUMO pathway components. In the present chapter, we introduce the SUMO Gene Network (SGN), a curated assembly of Arabidopsis thaliana genes that have been functionally associated with sumoylation, from SUMO pathway components to targets and interactors. The enclosed tutorial helps interpret and manage these datasets, and details bioinformatics tools that can be used for in silico-based hypothesis generation. The latter include tools for sumoylation site prediction, comparative genomics, and gene network analysis.
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Acknowledgments
This work was supported by FEDER through the Operational Competitiveness Program—COMPETE—and by national funds through the Foundation for Science and Technology—FCT—within the scope of project “SUMOdulator” [Refs. FCOMP-01-0124-FEDER-028459 and PTDC/BIA-PLA/3850/2012]. PHC was supported by the Fundação para a Ciência e a Tecnologia (FCT) [grant ref. SFRH/BD/44484/2008 and PTDC/BIA-PLA/3850/2012]. HA was supported by the “Genomics and Evolutionary Biology” project, co-financed by North Portugal Regional Operational Programme 2007/2013 (ON.2 – O Novo Norte), under the National Strategic Reference Framework (NSRF), through the European Regional Development Fund (ERDF).
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Castro, P.H., Santos, M.Â., Magalhães, A.P., Tavares, R.M., Azevedo, H. (2016). Bioinformatics Tools for Exploring the SUMO Gene Network. In: Lois, L., Matthiesen, R. (eds) Plant Proteostasis. Methods in Molecular Biology, vol 1450. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3759-2_23
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DOI: https://doi.org/10.1007/978-1-4939-3759-2_23
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