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GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.

Rachel S G Sealfon1, Matthew A Hibbs, Curtis Huttenhower

  • 1Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ, USA. sealfon@princeton.edu

BMC Bioinformatics
|October 13, 2006
PubMed
Summary

GOLEM is a new tool for exploring the Gene Ontology (GO) graph. It offers interactive visualization and analysis of gene annotations, supporting local files and offline use for biological data exploration.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • The Gene Ontology (GO) is crucial for genomic data analysis and biological knowledge organization.
  • Existing GO navigation tools often lack interactive graph views, offline capabilities, or integrated analysis and visualization.
  • Current tools are frequently web-based, requiring internet connectivity and limiting the use of local annotation files.

Purpose of the Study:

  • To develop a novel software tool for interactive exploration of the Gene Ontology (GO) hierarchy.
  • To address limitations of existing tools by providing both visualization and analysis functionalities.
  • To enable offline use of local GO and annotation files.

Main Methods:

  • Development of GOLEM (Gene Ontology Local Exploration Map), a visualization and analysis application.

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  • Implementation of dynamic graph expansion and focusing capabilities around user-selected terms.
  • Integration of rapid gene list analysis for identifying enriched GO terms.
  • Support for both local file usage and online access to the latest GO information.

    • Main Results:

    • GOLEM provides an interactively expandable graph-based view of the GO hierarchy.
    • The tool enables focused exploration of the GO graph structure.
    • GOLEM facilitates rapid analysis of gene lists to identify enriched GO terms.
    • Users can utilize local GO and annotation files or access online data.

    Conclusions:

    • GOLEM is a valuable tool for biologists needing to visualize GO hierarchy and identify enriched GO terms in gene sets.
    • The software supports offline analysis using local files, enhancing accessibility.
    • GOLEM is available as a free application and applet for broader use.