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PathExpress: a web-based tool to identify relevant pathways in gene expression data.

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.

Nucleic Acids Research
|June 26, 2007
PubMed
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PathExpress is a novel web tool for analyzing gene expression data from microarrays. It identifies key metabolic pathways linked to gene expression, aiding biological interpretation.

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Genomics

Background:

  • Gene expression data from microarrays requires interpretation to understand biological functions.
  • Identifying relevant metabolic pathways is crucial for functional genomics analysis.

Purpose of the Study:

  • To develop PathExpress, a web-based tool for interpreting gene expression data.
  • To link gene expression profiles to relevant metabolic pathways for functional context.

Main Methods:

  • PathExpress utilizes gene expression data and the KEGG Ligand database.
  • It assigns Enzyme Commission numbers to probe sets by homology.
  • Graphical pathway representation visualizes expressed genes within metabolic networks.

Main Results:

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  • PathExpress identifies the most relevant metabolic pathways associated with gene subsets.
  • The tool provides a functional context for visualized expressed genes.
  • Approximately 20% of probe sets are linked to metabolic pathways.

Conclusions:

  • PathExpress offers a valuable resource for interpreting microarray gene expression data.
  • The tool facilitates the understanding of biological functions through pathway analysis.
  • It is adaptable to various organisms and Affymetrix genome arrays.