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NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis.

Jill Cheng1, Shaw Sun, Adam Tracy

  • 1Affymetrix Corporation, Bioinformatics, 6550 Vallejo Street, Suite 100, Emeryville, CA 94608, USA. jill_cheng@affymetrix.com

Bioinformatics (Oxford, England)
|February 14, 2004
PubMed
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The NetAffx Gene Ontology (GO) Mining Tool visualizes microarray data by mapping gene expression to biological pathways. This interactive tool aids in understanding complex gene sets and their significance.

Area of Science:

  • Bioinformatics
  • Genomics
  • Systems Biology

Background:

  • Microarray analysis generates large datasets requiring effective interpretation.
  • Gene Ontology (GO) provides a standardized vocabulary for gene function.
  • Integrating expression data with GO facilitates biological discovery.

Purpose of the Study:

  • To present the NetAffx Gene Ontology (GO) Mining Tool.
  • To enable interactive visualization of GO graphs with microarray expression data.

Main Methods:

  • The tool accepts lists of Affymetrix probe sets.
  • It generates a GO graph visualized as a heat map.
  • The heat map is colored based on significance measurements.

Main Results:

Related Experiment Videos

  • The GO graph is interactive, allowing node traversal.
  • Nodes link to external web resources and relevant probe sets.
  • Thousands of genes can be viewed in a single interactive display.

Conclusions:

  • The NetAffx GO Mining Tool effectively combines biological annotation with gene expression data.
  • It offers an interactive platform for exploring complex genomic datasets.
  • This tool enhances the interpretation of microarray results by visualizing gene functions within biological pathways.