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Extending MapMan: application to legume genome arrays.

Nicolas Goffard1, Georg Weiller

  • 1ARC Centre of Excellence for Integrative Legume Research and Bioinformatics Laboratory, Genomic Interactions Group, Research School of Biological Sciences, Australian National University GPO Box 475, Canberra, ACT 2601, Australia.

Bioinformatics (Oxford, England)
|October 19, 2006
PubMed
Summary

This study extends MapMan, a gene expression visualization tool, to any organism using KEGG pathways. The system was successfully applied to model legumes, Glycine max and Medicago truncatula, for functional gene analysis.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Functional Genomics

Background:

  • MapMan was initially developed for Arabidopsis thaliana gene expression analysis within a functional context.
  • Gene classification relied on hierarchical categories known as BINs (Biological Interpretation Numbers).

Purpose of the Study:

  • To develop a bioinformatics system extending MapMan's functionality to any organism.
  • To create a new BIN structure based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.
  • To enable functional gene expression analysis for diverse species.

Main Methods:

  • A novel BIN structure was created using the KEGG database.
  • Gene sequences were assigned to the ontology via homology relationships in KEGG, COG, Swiss-Prot, and Gene Ontology databases.

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  • The system was tailored for GeneChips of Glycine max and Medicago truncatula, and a pathway identification module was developed.

    • Main Results:

    • MapMan was successfully extended to analyze gene expression in legumes (Glycine max and Medicago truncatula).
    • The homology-based assignment enabled functional context for gene expression data across different organisms.
    • A module for identifying relevant biological pathways was implemented.

    Conclusions:

    • The developed bioinformatics system provides a versatile platform for functional gene expression analysis in any organism.
    • This extension of MapMan facilitates comparative functional genomics and pathway discovery.
    • The system is publicly available for broader scientific application.