Publication: Beyond the bounds of orthology: functional inference from metagenomic context

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Title Beyond the bounds of orthology: functional inference from metagenomic context
Authors/Editors* Gregory Vey, Gabriel Moreno-Hagelsieb
Where published* Molecular BioSystems
How published* Journal
Year* 2010
Volume 6
Pages 1247–1254
Publisher The Royal Society of Chemistry
Keywords Base Sequence Computational Biology/methods Escherichia coli K12/genetics Gene Regulatory Networks Genome, Bacterial/genetics* Metagenome/genetics* Metagenomics/methods* Models, Genetic Operon/genetics Reproducibility of Results Seawater/microbiology* Water Microbiology
The effectiveness of the computational inference of function by genomic context is bounded by the diversity of known microbial genomes. Although metagenomes offer access to previously inaccessible organisms, their fragmentary nature prevents the conventional establishment of orthologous relationships required for reliably predicting functional interactions. We introduce a protocol for the prediction of functional interactions using data sources without information about orthologous relationships. To illustrate this process, we use the Sargasso Sea metagenome to construct a functional interaction network for the Escherichia coli K12 genome. We identify two reliability metrics, target intergenic distance and source interaction count, and apply them to selectively filter the predictions retained to construct the network of functional interactions. The resulting network contains 2297 nodes with 10 072 edges with a positive predictive value of 0.80. The metagenome yielded 8423 functional interactions beyond those found using only the genomic orthologs as a data source. This amounted to a 134% increase in the total number of functional interactions that are predicted by combining the metagenome and the genomic orthologs versus the genomic orthologs alone. In the absence of detectable orthologous relationships it remains feasible to derive a reliable set of predicted functional interactions. This offers a strategy for harnessing other metagenomes and homologs in general. Because metagenomes allow access to previously unreachable microorganisms, this will result in expanding the universe of known functional interactions thus furthering our understanding of functional organization.
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