Dataset Information

Integration of curated databases to identify genotype-phenotype associations.

ABSTRACT:

Background

The ability to rapidly characterize an unknown microorganism is critical in both responding to infectious disease and biodefense. To do this, we need some way of anticipating an organism's phenotype based on the molecules encoded by its genome. However, the link between molecular composition (i.e. genotype) and phenotype for microbes is not obvious. While there have been several studies that address this challenge, none have yet proposed a large-scale method integrating curated biological information. Here we utilize a systematic approach to discover genotype-phenotype associations that combines phenotypic information from a biomedical informatics database, GIDEON, with the molecular information contained in National Center for Biotechnology Information's Clusters of Orthologous Groups database (NCBI COGs).

Results

Integrating the information in the two databases, we are able to correlate the presence or absence of a given protein in a microbe with its phenotype as measured by certain morphological characteristics or survival in a particular growth media. With a 0.8 correlation score threshold, 66% of the associations found were confirmed by the literature and at a 0.9 correlation threshold, 86% were positively verified.

Conclusion

Our results suggest possible phenotypic manifestations for proteins biochemically associated with sugar metabolism and electron transport. Moreover, we believe our approach can be extended to linking pathogenic phenotypes with functionally related proteins.

SUBMITTER: Goh CS

PROVIDER: S-EPMC1630430 | biostudies-literature | 2006 Oct

REPOSITORIES: biostudies-literature

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Publications

Integration of curated databases to identify genotype-phenotype associations.

Goh Chern-Sing CS Gianoulis Tara A TA Liu Yang Y Li Jianrong J Paccanaro Alberto A Lussier Yves A YA Gerstein Mark M

BMC genomics 20061012

<h4>Background</h4>The ability to rapidly characterize an unknown microorganism is critical in both responding to infectious disease and biodefense. To do this, we need some way of anticipating an organism's phenotype based on the molecules encoded by its genome. However, the link between molecular composition (i.e. genotype) and phenotype for microbes is not obvious. While there have been several studies that address this challenge, none have yet proposed a large-scale method integrating curate ...[more]

PMID: 17038185

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Dataset Information

Integration of curated databases to identify genotype-phenotype associations.

Background

Results

Conclusion

Publications

Integration of curated databases to identify genotype-phenotype associations.

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