ArticleBMC microbiology2009
Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi.
Article in BMC microbiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed.
- A protein network refinement method based on module discovery and biological information.BMC bioinformatics · 2024Article
- Review
- A disease-related essential protein prediction model based on the transfer neural network.Frontiers in genetics · 2022Article
- DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction.BMC bioinformatics · 2021Article
- An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information.BMC bioinformatics · 2021Article
- CEGSO: Boosting Essential Proteins Prediction by Integrating Protein Complex, Gene Expression, Gene Ontology, Subcellular Localization and Orthology Information.Interdisciplinary sciences, computational life sciences · 2021Review
- A novel essential protein identification method based on PPI networks and gene expression data.BMC bioinformatics · 2021Article
- A Novel Collaborative Filtering Model-Based Method for Identifying Essential Proteins.Frontiers in genetics · 2021Review
- A Novel Model for Identifying Essential Proteins Based on Key Target Convergence Sets.Frontiers in genetics · 2021Article
- Method for Identifying Essential Proteins by Key Features of Proteins in a Novel Protein-Domain Network.Frontiers in genetics · 2021Article
- An Iterative Method for Predicting Essential Proteins Based on Multifeature Fusion and Linear Neighborhood Similarity.Frontiers in aging neuroscience · 2021Article
- A novel method to predict essential proteins based on tensor and HITS algorithm.Human genomics · 2020Article
- The Wolbachia Symbiont: Here, There and Everywhere.Results and problems in cell differentiation · 2020Article
- A Novel Computational Approach for Identifying Essential Proteins From Multiplex Biological Networks.Frontiers in genetics · 2020Article
- An iteration method for identifying yeast essential proteins from heterogeneous network.BMC bioinformatics · 2019Article
- Symbiosis Comes of age at the 10Applied and environmental microbiology · 2019Review
- Network-Based Metabolism-Centered Screening of Potential Drug Targets inFrontiers in cellular and infection microbiology · 2019Article
- Identification of essential proteins based on a new combination of topological and biological features in weighted protein-protein interaction networks.IET systems biology · 2018Article
- Mining Filarial Genomes for Diagnostic and Therapeutic Targets.Trends in parasitology · 2018Review
- Prediction of essential proteins based on subcellular localization and gene expression correlation.BMC bioinformatics · 2017Article
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5 authors.
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Abstract
backgroundWolbachia (wBm) is an obligate endosymbiotic bacterium of Brugia malayi, a parasitic filarial nematode of humans and one of the causative agents of lymphatic filariasis. There is a pressing need for new drugs against filarial parasites, such as B. malayi. As wBm is required for B. malayi development and fertility, targeting wBm is a promising approach. However, the lifecycle of neither B. malayi nor wBm can be maintained in vitro. To facilitate selection of potential drug targets we computationally ranked the wBm genome based on confidence that a particular gene is essential for the survival of the bacterium.
resultswBm protein sequences were aligned using BLAST to the Database of Essential Genes (DEG) version 5.2, a collection of 5,260 experimentally identified essential genes in 15 bacterial strains. A confidence score, the Multiple Hit Score (MHS), was developed to predict each wBm gene's essentiality based on the top alignments to essential genes in each bacterial strain. This method was validated using a jackknife methodology to test the ability to recover known essential genes in a control genome. A second estimation of essentiality, the Gene Conservation Score (GCS), was calculated on the basis of phyletic conservation of genes across Wolbachia's parent order Rickettsiales. Clusters of orthologous genes were predicted within the 27 currently available complete genomes. Druggability of wBm proteins was predicted by alignment to a database of protein targets of known compounds.
conclusionRanking wBm genes by either MHS or GCS predicts and prioritizes potentially essential genes. Comparison of the MHS to GCS produces quadrants representing four types of predictions: those with high confidence of essentiality by both methods (245 genes), those highly conserved across Rickettsiales (299 genes), those similar to distant essential genes (8 genes), and those with low confidence of essentiality (253 genes). These data facilitate selection of wBm genes for entry into drug design pipelines.
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