Cross Species Expression Analysis of Innate Immune Response

  • Yong Lu
  • Roni Rosenfeld
  • Gerard J. Nau
  • Ziv Bar-Joseph
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5541)


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.

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Dendritic Cell Innate Immune Response Edge Weight Markov Random Field Gene Node 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Yong Lu
    • 1
    • 3
  • Roni Rosenfeld
    • 1
  • Gerard J. Nau
    • 2
  • Ziv Bar-Joseph
    • 1
  1. 1.School of Computer ScienceCarnegie Mellon UniversityPittsburghUSA
  2. 2.Department of Molecular Genetics and BiochemistryUniversity of Pittsburgh Medical SchoolPittsburghUSA
  3. 3.Present address: Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonUSA

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