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.
Highlights
Arabidopsis (Arabidopsis thaliana) is the best studied plant species, the biological role of one-third of its proteins is still unknown
This homology-based transfer is a powerful approach for functional annotation of novel proteins, and one that can lead to erroneous inferences because similarity at the sequence level does not necessarily imply that proteins carry out the same function
Arabidopsis Protein Function Prediction demonstrating the performance of our method using cross-validation as a validation step, we investigated recent experimental evidence for our predictions
Summary
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. 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. Unraveling the biological processes in this species, is essential for the understanding of plant biology in general and for the transfer of this knowledge to other species. Fundamental to this goal is the functional annotation of Arabidopsis proteins.
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