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Web-based analysis of the mouse transcriptome using Genevestigator.

Oliver Laule1, Matthias Hirsch-Hoffmann, Tomas Hruz

  • 1Institute of Plant Sciences, ETH Zurich, 8092 Zurich, Switzerland. ola@ethz.ch

BMC Bioinformatics
|June 23, 2006
PubMed
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Genevestigator provides a user-friendly platform for analyzing gene expression patterns from microarray data. This tool aids researchers in generating testable hypotheses for laboratory experiments by querying extensive gene expression datasets.

Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Gene function analysis is complex, often requiring extensive laboratory and computational experiments.
  • Effective experimental design relies on prior knowledge and hypothesis generation.
  • Meta-analysis of expression data and annotation libraries can guide hypothesis formulation for gene and network function.

Purpose of the Study:

  • To introduce Genevestigator, a microarray database and analysis system.
  • To enable biologists with limited computational expertise to query gene expression data.
  • To facilitate context-driven queries for understanding gene expression patterns.

Main Methods:

  • Development and utilization of the Genevestigator platform.
  • Manual curation and quality control of 3110 mouse Affymetrix arrays from public repositories.

Related Experiment Videos

  • Implementation of an annotation library with categories for anatomy, developmental stages, stimuli, and genetic backgrounds.

    • Main Results:

    • Genevestigator allows context-driven queries for gene expression analysis.
    • The system supports queries across diverse biological contexts (e.g., anatomy, development, stimuli, genetics).
    • Biological scenarios demonstrate the system's ability to yield meaningful, literature-substantiated results.

    Conclusions:

    • The Genevestigator-Mouse database provides biologically meaningful results.
    • The platform is accessible online at https://www.genevestigator.ethz.ch.
    • Genevestigator simplifies gene expression data analysis for hypothesis generation.