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

Despite increasing availability of sequenced genomes, accurate characterization of gene functions is needed to close the genotype-phenotype gap. Recent advances in gene function prediction rely on ensemble approaches that integrate the results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We present Neighbor Counting Ensemble, a gene function prediction method which integrates eleven gene co-function networks for Arabidopsis thaliana, and produces more accurate gene function predictions for a larger fraction of genes with unknown function. We used these predictions 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, available at http://www.gene2function.de/ensemblenet.html.