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In Silico Tools for Gene Discovery pp 141–157Cite as

Application of Gene Ontology to Gene Identification

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 760))

Abstract

Candidate gene identification deals with associating genes to underlying biological phenomena, such as diseases and specific disorders. It has been shown that classes of diseases with similar phenotypes are caused by functionally related genes. Currently, a fair amount of knowledge about the functional characterization can be found across several public databases; however, functional descriptors can be ambiguous, domain specific, and context dependent. In order to cope with these issues, the Gene Ontology (GO) project developed a bio-ontology of broad scope and wide applicability. Thus, the structured and controlled vocabulary of terms provided by the GO project describing the biological roles of gene products can be very helpful in candidate gene identification approaches. The method presented here uses GO annotation data in order to identify the most meaningful functional aspects occurring in a given set of related gene products. The method measures this meaningfulness by calculating an e-value based on the frequency of annotation of each GO term in the set of gene products versus the total frequency of annotation. Then after selecting a GO term related to the underlying biological phenomena being studied, the method uses semantic similarity to rank the given gene products that are annotated to the term. This enables the user to further narrow down the list of gene products and identify those that are more likely of interest.

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Author information

Authors and Affiliations

  1. Department of Informatics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal

    Hugo P. Bastos, Bruno Tavares, Catia Pesquita, Daniel Faria & Francisco M. Couto

Authors
  1. Hugo P. Bastos
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  2. Bruno Tavares
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  3. Catia Pesquita
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  4. Daniel Faria
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  5. Francisco M. Couto
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Corresponding author

Correspondence to Hugo P. Bastos .

Editor information

Editors and Affiliations

  1. Royal Prince Alfred Hospital, Dept. of Molecular & Clinical Genetics, University of Sydney, Missenden Road, Camperdown, 2050, New South Wales, Australia

    Bing Yu

  2. Royal Prince Alfred Hospital, Dept. Molecular & Clinical Genetics, University of Sydney, Missenden Road, Camperdown, 2050, New South Wales, Australia

    Marcus Hinchcliffe

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Bastos, H.P., Tavares, B., Pesquita, C., Faria, D., Couto, F.M. (2011). Application of Gene Ontology to Gene Identification. In: Yu, B., Hinchcliffe, M. (eds) In Silico Tools for Gene Discovery. Methods in Molecular Biology, vol 760. Humana Press. https://doi.org/10.1007/978-1-61779-176-5_9

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  • DOI: https://doi.org/10.1007/978-1-61779-176-5_9

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-175-8

  • Online ISBN: 978-1-61779-176-5

  • eBook Packages: Springer Protocols

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