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Cross Species Expression Analysis of Innate Immune Response

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Research in Computational Molecular Biology (RECOMB 2009)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5541))

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Abstract

The innate immune response is the first line of host defense against infections. This system employs a number of different types of cells which in turn activate different sets of genes. Microarray studies of human and mouse cells infected with various pathogens identified hundreds of differentially expressed genes. However, combining these datasets to identify common and unique response patterns remained a challenge. We developed methods based on probabilistic graphical models to combine expression experiments across species, cells and pathogens. Our method analyzes homologous genes in different species concurrently overcoming problems related to noise and orthology assignments. Using our method we identified both core immune response genes and genes that are activated in macrophages in both human and mouse but not in dendritic cells, and vice versa. Our results shed light on immune response mechanisms and on the differences between various types of cells that are used to fight infecting bacteria.

Supporting website: http://www.cs.cmu.edu/~lyongu/pub/immune/

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Author information

Authors and Affiliations

  1. School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA

    Yong Lu, Roni Rosenfeld & Ziv Bar-Joseph

  2. Department of Molecular Genetics and Biochemistry, University of Pittsburgh Medical School, Pittsburgh, PA 15213, USA

    Gerard J. Nau

  3. Present address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA

    Yong Lu

Authors
  1. Yong Lu
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  2. Roni Rosenfeld
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  3. Gerard J. Nau
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  4. Ziv Bar-Joseph
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Editor information

Editors and Affiliations

  1. Computer Science Department, James H. Clark Center, 318 Campus Drive, RM S266, CA 94305-5428,, Stanford, USA

    Serafim Batzoglou

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© 2009 Springer-Verlag Berlin Heidelberg

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Lu, Y., Rosenfeld, R., Nau, G.J., Bar-Joseph, Z. (2009). Cross Species Expression Analysis of Innate Immune Response. In: Batzoglou, S. (eds) Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science(), vol 5541. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02008-7_7

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  • DOI: https://doi.org/10.1007/978-3-642-02008-7_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02007-0

  • Online ISBN: 978-3-642-02008-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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