ArticleBMC genomics2006
Integration of curated databases to identify genotype-phenotype associations.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes.BMC bioinformatics · 2021Article
- Identifying genotype-phenotype relationships in biomedical text.Journal of biomedical semantics · 2017Article
- Comparative Genomics ofFrontiers in plant science · 2017Article
- The landscape of microbial phenotypic traits and associated genes.Nucleic acids research · 2016Article
- COPD Hospitalization Risk Increased with Distinct Patterns of Multiple Systems Comorbidities Unveiled by Network Modeling.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2014Article
- Identification of logic relationships between genes and subtypes of non-small cell lung cancer.PloS one · 2014Article
- Knowledge management and informatics considerations for comparative effectiveness research: a case-driven exploration.Medical care · 2013Article
- The laboratory-clinician team: a professional call to action to improve communication and collaboration for optimal patient care in chromosomal microarray testing.Journal of genetic counseling · 2012Article
- Engineering ecosystems and synthetic ecologies.Molecular bioSystems · 2012Review
- In-silico identification of phenotype-biased functional modules.Proteome science · 2012Article
- Phenotypic information in genomic variant databases enhances clinical care and research: the International Standards for Cytogenomic Arrays Consortium experience.Human mutation · 2012Article
- MimoSA: a system for minimotif annotation.BMC bioinformatics · 2010Article
- A PubMed-wide associational study of infectious diseases.PloS one · 2010Article
- Biological Resource Centers and Systems Biology.Bioscience · 2009Article
- Article
- Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes.Genome biology · 2009Article
- Microbial genotype-phenotype mapping by class association rule mining.Bioinformatics (Oxford, England) · 2008Article
- A collaborative knowledge base for cognitive phenomics.Molecular psychiatry · 2008Article
- An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.PLoS computational biology · 2006Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundThe 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).
resultsIntegrating 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.
conclusionOur 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.
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