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Cardiovascular Genomics

Volume 573 of the series Methods in Molecular Biology™ pp 329-345

Date:

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

  • Paul FisherAffiliated withSchool of Computer Science, University of Manchester
  • , Harry NoyesAffiliated withSchool of Biological Sciences, University of Liverpool
  • , Stephen KempAffiliated withSchool of Biological Sciences, University of Liverpool
  • , Robert StevensAffiliated withSchool of Computer Science, University of Manchester
  • , Andrew BrassAffiliated withSchool of Computer Science, University of Manchester

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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