title: Bioinformatics Tools for Exploring the SUMO Gene Network.
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.
authors.affiliation: Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
authors.forename: Pedro Humberto
authors.initials: PH
authors.lastname: Castro
authors.affiliation: Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.|CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
authors.forename: Miguel Ângelo
authors.initials: MÂ
authors.lastname: Santos
authors.affiliation: Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.|CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
authors.forename: Alexandre Papadopoulos
authors.initials: AP
authors.lastname: Magalhães
authors.affiliation: Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
authors.forename: Rui Manuel
authors.initials: RM
authors.lastname: Tavares
authors.affiliation: CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal. hazevedo@cibio.up.pt.
authors.forename: Herlânder
authors.initials: H
authors.lastname: Azevedo
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D053263:Gene Regulatory Networks / Q000235:genetics*; D023281:Genomics / Q000379:methods; D040901:Proteomics / Q000379:methods; D025841:Small Ubiquitin-Related Modifier Proteins / Q000235:genetics*; D058207:Sumoylation / Q000235:genetics*
chemical_list: D025841:Small Ubiquitin-Related Modifier Proteins
keywords: Arabidopsis; Bioinformatics; Data mining; Functional categorization; Gene expression; Gene network; Post-translational modification; Small ubiquitin-related modifier (SUMO)