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Combinatorial Use of Short Probes for Differential Gene Expression Profiling

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Algorithms in Bioinformatics (WABI 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2452))

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Abstract

Motivation: Gene chips or microarrays have made it possible to perform large-scale gene-expression experiments at the wholegenome level. To reduce the cost and identify genes that are differentially expressed between samples from hybridization signal intensity, we are proposing a suite of methods to use a relatively small number of short oligo probes for whole-genome or tissue-specific gene-expression studies. Results: We present methods to choose a set of short oligos to design a genome or tissue-specific biochip and then to solve a set of equations for gene-expression levels to determine genes that are differentially expressed between samples. The methods have been tested to define a set of 4,000 8mers as probes to identify genes that have fold changes for more than 6,000 identified yeast ORFs. These methods can also be expanded to design genome-specific or tissue-specific biochips for other organisms with full gene-sequence information.

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Author information

Authors and Affiliations

  1. Bioinformatics Program, North Carolina State University, 27695, Raleigh, NC, USA

    Liling L. Warren & Ben Hui Liu

  2. Bio-informatics Group Inc., 27511, Cary, NC, USA

    Liling L. Warren & Ben Hui Liu

Authors
  1. Liling L. Warren
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  2. Ben Hui Liu
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Editor information

Editors and Affiliations

  1. IMIM-UPF-CRG, Dr. Aiguader 80, 08003, Barcelona, Spain

    Roderic Guigó

  2. Department of Computer Science, University of California, 95616, Davis, CA, USA

    Dan Gusfield

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© 2002 Springer-Verlag Berlin Heidelberg

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Warren, L.L., Liu, B.H. (2002). Combinatorial Use of Short Probes for Differential Gene Expression Profiling. In: Guigó, R., Gusfield, D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45784-4_37

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  • DOI: https://doi.org/10.1007/3-540-45784-4_37

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-44211-0

  • Online ISBN: 978-3-540-45784-8

  • eBook Packages: Springer Book Archive

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