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New Phytol. 2018 Mar;217(4):1521-1534. doi: 10.1111/nph.14921. Epub 2017 Dec 4.

Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana.

Author information

1
Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam, 14476, Germany.
2
Institut für Medizinische Informatik, Universitätsmedizin Göttingen, Robert-Koch-Str. 40, Göttingen, 37075, Germany.
3
Department of Plant Biotechnology and Bioinformatics, VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, Gent, B-9052, Belgium.
4
Rijk Zwaan Breeding BV, Burgemeester Crezéelaan 40, PO Box 40, De Lier, 2678 ZG, the Netherlands.
5
Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, 14476, Germany.
6
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.

Abstract

Recent advances in gene function prediction rely on ensemble approaches that integrate results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We have explored and compared two methods to integrate 10 gene co-function networks for Arabidopsis thaliana and demonstrate how the integration of these networks produces more accurate gene function predictions for a larger fraction of genes with unknown function. These predictions were used to identify genes involved in mitochondrial complex I formation, and for five of them, we confirmed the predictions experimentally. The ensemble predictions are provided as a user-friendly online database, EnsembleNet. The methods presented here demonstrate that ensemble gene function prediction is a powerful method to boost prediction performance, whereas the EnsembleNet database provides a cutting-edge community tool to guide experimentalists.

KEYWORDS:

Arabidopsis thaliana ; co-function network; complex I; ensemble prediction; gene function prediction

PMID:
29205376
DOI:
10.1111/nph.14921

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