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NetAffx: Affymetrix probesets and annotations.

Guoying Liu1, Ann E Loraine, Ron Shigeta

  • 1Department of Bioinformatics, Affymetrix, Inc, 6550 Vallejo Street, Suite 100, Emeryville, CA 94608, USA. guoying_liu@affymetrix.com

Nucleic Acids Research
|January 10, 2003
PubMed
Summary
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NetAffx provides detailed annotations for Affymetrix GeneChip microarray probesets, integrating sequence data with biological information for enhanced genomic analysis.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Affymetrix GeneChip microarrays are widely used for gene expression analysis.
  • Comprehensive annotation of probesets is crucial for accurate interpretation of microarray data.

Purpose of the Study:

  • To describe the NetAffx database and its annotation features for Affymetrix GeneChip probesets.
  • To highlight the integration of diverse data types for biological context.

Main Methods:

  • Collection and integration of static probeset information.
  • Extraction of sequence annotations from public databases.
  • Application of public domain programs and Hidden Markov Models (HMMs) for protein sequence analysis.
  • Development of interactive genomic maps for sequence data visualization.

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Main Results:

  • NetAffx provides detailed probe and consensus sequences for each probeset.
  • Sequence annotations include Gene Ontology (GO) terms, predicted protein domains, orthologous sequences, and pathway links.
  • Interactive maps display sequence data within genomic context for larger chip sets.
  • Links to public databases such as UniGene, LocusLink, SWISS-PROT, and OMIM are provided.

Conclusions:

  • NetAffx serves as a comprehensive resource for annotating Affymetrix GeneChip probesets.
  • The integrated annotations facilitate deeper understanding of gene function and biological pathways.
  • NetAffx enhances the utility of microarray data by providing rich contextual information.