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The Innate Immune Database (IIDB).

Martin Korb1, Aistair G Rust, Vesteinn Thorsson

  • 1Institute for Systems Biology, 1441 North 34thStreet, Seattle, Washington 98103-8904, USA. mkorb@systemsbiology.org

BMC Immunology
|March 7, 2008
PubMed
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This study introduces the Innate Immune Database (IIDB), a free online resource for analyzing gene regulation in immune responses. It aids researchers in understanding the complex network controlling macrophage reactions to pathogens.

Area of Science:

  • Immunology
  • Systems Biology
  • Bioinformatics

Background:

  • Microarray experiments profiled C57/BL6 mouse bone marrow macrophage responses to toll-like receptor stimuli.
  • Expression data is publicly available, forming the basis for further research.
  • Focus on innate immunity and macrophage responses to pathogens.

Purpose of the Study:

  • Develop a comprehensive database of predicted transcription factor binding sites and genomic features for murine immune genes.
  • Provide a freely accessible web resource for the research community.
  • Facilitate the study of gene regulatory networks in innate immune responses.

Main Methods:

  • Constructed a gene-indexed database with genomic region annotations.
  • Utilized six computational algorithms to predict transcription factor binding sites using TRANSFAC Position Weight Matrices.

Related Experiment Videos

  • Integrated microarray co-expression clusters and web-based query/analysis tools.
  • Developed a customized Argo genome browser for visualization.

    • Main Results:

    • Created a database of over 2000 murine immune genes with predicted transcription factor binding sites.
    • Achieved over 50% concordance between predicted ATF3 binding sites and experimental ChIP-chip data.
    • Database includes query, analysis, and visualization facilities.

    Conclusions:

    • The Innate Immune Database (IIDB) is presented as a valuable community resource.
    • Facilitates research into gene regulatory systems underlying innate immune responses.
    • Accessible online for immunologists studying pathogen responses.