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Microarray Probe Mapping and Annotation in Cross-Species Comparative Toxicogenomics

  • John N. Calley
  • William B. Mattes
  • Timothy P. Ryan
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 460)

Summary

Genomics-based tools, such as microarrays, do appear to offer promise in evaluating the relevance of one species to another in terms of molecular and cellular response to a given treatment. However, to fulfill this promise the individual end points (i.e., the genes, proteins, or mRNAs) measured in one species must be mapped to corresponding end points in another species. Several approaches, along with their strengths and weaknesses, are described in this chapter. A sequential approach is described that first makes use of a “Genome To Genome Through Orthology” method, where probe sequences for a given species are mapped into full-length sequences for that species, associated with the locus for those sequences and then into a second species by consulting orthology resources. The second step supplements these results by mapping the probe sequences for the given species into the best matching transcript from any organism, which then are mapped into the appropriate native locus and finally into the second species via an orthology resource. The results of this method are given for an experiment comparing the transcriptional response of canine liver to phenobarbital with that of rat liver.

Key Words

annotation bioinformatics cross-species genomics microarray mRNA 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • John N. Calley
    • 1
  • William B. Mattes
    • 2
  • Timothy P. Ryan
    • 1
  1. 1.Department of Integrative BiologyEli Lilly and CompanyGreenfield
  2. 2.Department of ToxicologyThe Critical Path InstituteRockvilleMaryland

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