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Updated: Jul 13, 2026

Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer
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AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets.

Hongfang Liu1, Barry R Zeeberg, Gang Qu

  • 1Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. hl224@georgetown.edu

Bioinformatics (Oxford, England)
|July 31, 2007
PubMed
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AffyProbeMiner corrects inaccurate probe sets on Affymetrix microarrays, ensuring accurate gene expression analysis. This tool re-groups and re-maps probes for reliable mRNA transcript measurement.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Affymetrix microarrays measure global mRNA expression using probe sets.
  • Original probe groupings can be inaccurate due to evolving genomic knowledge.
  • Inaccurate probe sets lead to errors in microarray data analysis.

Purpose of the Study:

  • To develop a tool for correcting inaccurate Affymetrix microarray probe sets.
  • To improve the accuracy of gene expression analysis from microarray data.

Main Methods:

  • AffyProbeMiner uses RefSeq and GenBank transcripts to regroup probes into transcript-consistent sets.
  • Probe sets are remapped to their correct mRNA transcripts.
  • A web service is available for custom array remapping.

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Main Results:

  • AffyProbeMiner re-groups and re-maps probes for accurate hybridization.
  • Approximately 65.6% of probe sets on the HG-U133A chip were affected by remapping.
  • The tool is computationally efficient, flexible, and user-friendly.

Conclusions:

  • AffyProbeMiner ensures accurate measurement of mRNA transcripts by correcting probe set definitions.
  • The tool enhances the reliability of Affymetrix microarray experiments.
  • Pre-computed data and a web service are freely available.