APMA Database for Affymetrix Target Sequences Mapping, Quality Assessment and Expression Data Mining

  • Yuriy Orlov
  • Jiangtao Zhou
  • Joanne Chen
  • Atif Shahab
  • Vladimir Kuznetsov
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4774)

Abstract

We have developed an online database APMA (Affymetrix Probe Mapping and Annotation) for interactive presentation, search and visualization of Affymetrix target sequences mapping and annotation <http://apma.bii.a-star.edu.sg>. APMA contains revised genome localization of the Affymetrix U133 GeneChip initial (target) probe sequences. We designed APMA to use it as a filter before data analysis and data mining so that noise expression signals, false correlations and false gene expression patterns can be reduced. Discrepancies found in probeset annotation and target sequence mapping account for up to 30% of probesets, including about 25% of Affymetrix probesets derived from target sequences overlapped interspersed repeats and 1.8% of original target sequences with erroneous orientation of the sequences. 86% of U133 target sequences passed our quality-control filtering.

Keywords

Affymetrix U133 database target sequences cross-hybridization mapping genome repeats errors classification recognition data mining 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Yuriy Orlov
    • 1
  • Jiangtao Zhou
    • 1
  • Joanne Chen
    • 2
  • Atif Shahab
    • 1
    • 2
  • Vladimir Kuznetsov
    • 1
  1. 1.Genome Institute of Singapore, 60 Biopolis Street, Genome, 138672Singapore
  2. 2.Bioinformatics Institute, 30 Biopolis Street, Matrix, 138671Singapore

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