AffyProbeMiner -- a web resource for computing or retrieving accurately redefined Affymetrix probe sets

What you can do:
Explore redefined Affymetrix microarray data.
Highlights:
  • AffyProbeMiner is a computationally efficient platform-independent tool that uses all RefSeq mature RNA protein coding transcripts and validated complete coding sequences in GenBank to (1) regroup the individual probes into consistent probe sets and (2) remap the probe sets to the correct sets of mRNA transcripts.
  • The individual probes are grouped into probe sets that are 'transcript-consistent' in that they hybridize to the same mRNA transcript (or transcripts) and, therefore, measure the same entity (or entities).
  • About 65.6% of the probe sets on the HG-U133A chip were affected by the remapping. Pre-computed regrouped and remapped probe sets for many Affymetrix microarrays are made freely available at the AffyProbeMiner web site.
  • Alternatively, we provide a web service that enables the user to perform the remapping for any type of short-oligo commercial or custom array that has an Affymetrix-format Chip Definition File (CDF).
  • Important features that differentiate AffyProbeMiner from other approaches are flexibility in the handling of splice variants, computational efficiency, extensibility, customizability and user-friendliness of the interface.
Keywords:
  • Oligonucleotide Array Sequence Analysis
  • Affymetrix
  • Microarray
  • Probe Sets
  • Gene Chips
This record last updated: 04-18-2014

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