Geptop: A Gene Essentiality Prediction Tool for Sequenced Bacterial Genomes Based on Orthology and Phylogeny

Abstract

Integrative genomics predictors, which score highly in predicting bacterial essential genes, would be unfeasible in most species because the data sources are limited. We developed a universal approach and tool designated Geptop, based on orthology and phylogeny, to offer gene essentiality annotations. In a series of tests, our Geptop method yielded higher area under curve (AUC) scores in the receiver operating curves than the integrative approaches. In the ten-fold cross-validations among randomly upset samples, Geptop yielded an AUC of 0.918, and in the cross-organism predictions for 19 organisms Geptop yielded AUC scores between 0.569 and 0.959. A test applied to the very recently determined essential gene dataset from the Porphyromonas gingivalis, which belongs to a phylum different with all of the above 19 bacterial genomes, gave an AUC of 0.77. Therefore, Geptop can be applied to any bacterial species whose genome has been sequenced. Compared with the essential genes uniquely identified by the lethal screening, the essential genes predicted only by Gepop are associated with more protein-protein interactions, especially in the three bacteria with lower AUC scores (<0.7). This may further illustrate the reliability and feasibility of our method in some sense. The web server and standalone version of Geptop are available at http://cefg.uestc.edu.cn/geptop/ free of charge. The tool has been run on 968 bacterial genomes and the results are accessible at the website.

Bacterial protein interaction networks: connectivity is ruled by gene conservation, essentiality and function

“…We believe that the observations we have presented here can have implications both for the prediction of gene essentiality, based on the knowledge of PPI networks, and for the prediction of interactions between proteins, based on genetic information [21,45]. It is interesting to note that our results are consistent with a previous study based on inferred bacterial co-conserved networks based on phylogenetic profiles [27].…”

Defining Essential Genes and Identifying Virulence Factors of Porphyromonas gingivalis by Massively Parallel Sequencing of Transposon Libraries (Tn-seq)

“…The genes identified during our study as essential have been deposited and curated in the DEG (24). An in silico bioinformatic analysis was performed using the P. gingivalis essential gene data as validation for the program GepTop, which is a tool for predicting gene essentiality in sequenced genomes (30). …”

Review Selectional versus mutational mechanism underlying genomic features of bacterial strand asymmetry: a case study in Clostridium acetobutylicum

“…We predicted essential genes using the Geptop webserver, which first provided an online platform for detecting essential genes (http://cefg.uestc.edu.cn/geptop/) (Wei et al, 2013). We submitted the entire proteome for a bacterial species in FASTA format.…”