A Systematic Strategy for the Discovery of Candidate Genes Responsible for Phenotypic Variation

  • Paul Fisher
  • Harry Noyes
  • Stephen Kemp
  • Robert Stevens
  • Andrew Brass
Part of the Methods in Molecular Biology™ book series (MIMB, volume 573)

Abstract

It is increasingly common to combine genome-wide expression data with quantitative trait mapping data to aid in the search for sequence polymorphisms responsible for phenotypic variation. By joining these complex but different data types at the level of the biological pathway, we can take advantage of existing biological knowledge to systematically identify possible mechanisms of genotype–phenotype interaction. With the development of web services and workflows, this process can be made rapid and systematic. Our methodology was applied to a use case of resistance to African trypanosomiasis in mice. Workflows developed in this investigation, including a guide to loading and executing them with example data, are available at http://www.myexperiment.org/users/43/workflows.

Key words

Genotype phenotype QTL microarray workflows web services 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Paul Fisher
    • 1
  • Harry Noyes
    • 2
  • Stephen Kemp
    • 2
  • Robert Stevens
    • 1
  • Andrew Brass
    • 1
  1. 1.School of Computer Science, University of ManchesterManchesterUK
  2. 2.School of Biological Sciences, University of LiverpoolLiverpoolUK

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