ArticleNucleic acids research2005
Prediction of functional modules based on comparative genome analysis and Gene Ontology application.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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57 citing papers in PubMed.
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- Computational Methods for Identifying Similar Diseases.Molecular therapy. Nucleic acids · 2019Review
- Protein-protein interaction prediction using a hybrid feature representation and a stacked generalization scheme.BMC bioinformatics · 2019Article
- VarWatch-A stand-alone software tool for variant matching.PloS one · 2019Article
- An improved approach to infer protein-protein interaction based on a hierarchical vector space model.BMC bioinformatics · 2018Article
- Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach.BMC systems biology · 2018Article
- Developing a similarity searching module for patient safety event reporting system using semantic similarity measures.BMC medical informatics and decision making · 2017Article
- An improved method for functional similarity analysis of genes based on Gene Ontology.BMC systems biology · 2016Article
- SGFSC: speeding the gene functional similarity calculation based on hash tables.BMC bioinformatics · 2016Article
- Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses.Scientific reports · 2016Article
- Missing value imputation for microRNA expression data by using a GO-based similarity measure.BMC bioinformatics · 2016Article
- Revisiting operons: an analysis of the landscape of transcriptional units in E. coli.BMC bioinformatics · 2015Article
- Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton.BMC genomics · 2014Article
- HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins.PloS one · 2014Article
- An integrative approach for measuring semantic similarities using gene ontology.BMC systems biology · 2014Article
- Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2014Article
- An efficient weighted graph strategy to identify differentiation associated genes in embryonic stem cells.PloS one · 2013Article
- Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.PLoS computational biology · 2013Article
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5 authors.
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Abstract
We present a computational method for the prediction of functional modules encoded in microbial genomes. In this work, we have also developed a formal measure to quantify the degree of consistency between the predicted and the known modules, and have carried out statistical significance analysis of consistency measures. We first evaluate the functional relationship between two genes from three different perspectives--phylogenetic profile analysis, gene neighborhood analysis and Gene Ontology assignments. We then combine the three different sources of information in the framework of Bayesian inference, and we use the combined information to measure the strength of gene functional relationship. Finally, we apply a threshold-based method to predict functional modules. By applying this method to Escherichia coli K12, we have predicted 185 functional modules. Our predictions are highly consistent with the previously known functional modules in E.coli. The application results have demonstrated that our approach is highly promising for the prediction of functional modules encoded in a microbial genome.
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