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Microbial Gene Essentiality: Protocols and Bioinformatics pp 369–381Cite as

Statistical Analysis of Fitness Data Determined by TAG Hybridization on Microarrays

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 416))

Abstract

TAG, or bar-code, microarrays allow measurement of the oligonucleotide sequences (TAGs) that mark each strain of deletion mutants in the Saccharomyces cerevisiae yeast knockout (YKO) collection. Comparison of genomic DNA from pooled YKO samples allows estimation of relative abundance of TAGs marking each deletion strain. Features of TAG hybridizations create unique challenges for analysis. Analysis is complicated by the presence of two TAGs in most YKO strains and the hybridization behavior of TAGs that may differ in sequence from array probes. The oligonucleotide size of labeled TAGs also results in difficulty with contaminating sequences that cause reduced specificity. We present methods for analysis that approach these unique features of TAG hybridizations.

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Author information

Authors and Affiliations

  1. United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD

    Brian D. Peyser

  2. Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD

    Rafael Irizarry

  3. Department of Molecular Biology and Genetics, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD

    Forrest A. Spencer

Authors
  1. Brian D. Peyser
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  2. Rafael Irizarry
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  3. Forrest A. Spencer
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Editor information

Editors and Affiliations

  1. Burnham Institute for Medical Research, La Jolla, California

    Andrei L. Osterman

  2. Fellowship for Interpretation of Genomes (FIG), Burr Ridge, Illinois

    Svetlana Y. Gerdes

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

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Peyser, B.D., Irizarry, R., Spencer, F.A. (2008). Statistical Analysis of Fitness Data Determined by TAG Hybridization on Microarrays. In: Osterman, A.L., Gerdes, S.Y. (eds) Microbial Gene Essentiality: Protocols and Bioinformatics. Methods in Molecular Biology™, vol 416. Humana Press. https://doi.org/10.1007/978-1-59745-321-9_25

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  • DOI: https://doi.org/10.1007/978-1-59745-321-9_25

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-378-7

  • Online ISBN: 978-1-59745-321-9

  • eBook Packages: Springer Protocols

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