title: Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources.
abstract: Although Arabidopsis (Arabidopsis thaliana) is the best studied plant species, the biological role of one-third of its proteins is still unknown. We developed a probabilistic protein function prediction method that integrates information from sequences, protein-protein interactions, and gene expression. The method was applied to proteins from Arabidopsis. Evaluation of prediction performance showed that our method has improved performance compared with single source-based prediction approaches and two existing integration approaches. An innovative feature of our method is that it enables transfer of functional information between proteins that are not directly associated with each other. We provide novel function predictions for 5,807 proteins. Recent experimental studies confirmed several of the predictions. We highlight these in detail for proteins predicted to be involved in flowering and floral organ development.
authors.affiliation: Biometris, Wageningen University and Research Centre, 6700 AC Wageningen, The Netherlands.
authors.forename: Yiannis A I
authors.initials: YA
authors.lastname: Kourmpetis
authors.forename: Aalt D J
authors.initials: AD
authors.lastname: van Dijk
authors.forename: Roeland C H J
authors.initials: RC
authors.lastname: van Ham
authors.forename: Cajo J F
authors.initials: CJ
authors.lastname: ter Braak
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism*; D019540:Area Under Curve; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D035264:Flowers / Q000196:embryology / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D008390:Markov Chains; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D038081:Organogenesis / Q000235:genetics; D015203:Reproducibility of Results
chemical_list: D029681:Arabidopsis Proteins