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Integrative analysis of the mouse embryonic transcriptome.

Amar V Singh1, Kenneth B Knudsen, Thomas B Knudsen

  • 1Department of Molecular, Cellular and Craniofacial Biology, University of Louisville, School of Dentistry, Louisville, KY 40202, USA.

Bioinformation
|June 29, 2007
PubMed
Summary
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A new knowledge management system, Birth Defects Systems Manager (BDSM), integrates public microarray data to create a gene-expression signature library for studying embryonic development and birth defects. This enables comparative bioinformatics analysis of developmental processes.

Area of Science:

  • Developmental Biology
  • Teratology
  • Bioinformatics
  • Genomics

Background:

  • Monitoring global gene expression is crucial for understanding embryonic development.
  • Developmental biology and teratology require accessible reference libraries of gene-expression signatures.
  • Existing microarray data is highly distributed, necessitating data integration tools.

Purpose of the Study:

  • To describe tools for seamless data integration within the Birth Defects Systems Manager (BDSM) knowledge management system.
  • To develop a method for mining public microarray data for developmental health and disease research.
  • To create a gene-expression signature library for benchmarking embryonic transcriptome regulation.

Main Methods:

  • Utilized the QueryBDSM module and associated tools (MetaSample, MetaChip, CIAeasy) for data integration.

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  • Integrated published microarray data series from diverse laboratories, experiments, and platforms.
  • Focused on mouse embryo datasets covering various organ systems and developmental stages.

    • Main Results:

    • Successfully integrated diverse microarray data into the BDSM library.
    • Resolved a gene-expression signature for 346 genes that accurately classified samples by organ system and developmental sequence.
    • Demonstrated the potential of BDSM for deciphering developmental processes through comparative bioinformatics.

    Conclusions:

    • An integrative analysis of global gene expression in developing embryos is foundational for a reference library of signaling pathways.
    • The BDSM approach facilitates comparative bioinformatics analysis of embryological systems at risk for defects.
    • Developed tools are freely available to support research in developmental biology and teratology.