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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays.

Ramil N Nurtdinov1, Mikhail O Vasiliev, Anna S Ershova

  • 1Departament of Bioengineering and Bioinformatics, MV Lomonosov Moscow State University, Vorbyevy Gory 1-73, Moscow 119992, Russia. ramil@bioinf.fbb.msu.ru

Nucleic Acids Research
|November 13, 2009
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Summary

Affymetrix gene expression arrays can yield inaccurate results due to probe issues. PLANdbAffy identifies reliable probes by aligning sequences to the human genome, improving gene expression analysis accuracy.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Standard Affymetrix technology relies on probe hybridization for gene expression measurement.
  • Probe signal intensity may not accurately reflect true gene expression levels due to various factors.

Purpose of the Study:

  • To develop a comprehensive database, PLANdbAffy, for assessing Affymetrix probe reliability.
  • To identify probes that accurately map to transcript-coding regions and improve gene expression analysis.

Main Methods:

  • Alignment of Affymetrix probe sequences from five human microarrays to the human genome.
  • Identification of probes mapping to correct transcript-coding regions and orientation.
  • Integration of probe alignment data, mRNA/EST sequences, and Single Nucleotide Polymorphisms (SNPs).

Main Results:

  • PLANdbAffy database created, containing alignment results for Affymetrix probes.
  • Identified reliable probes matching transcript-coding regions and orientation.
  • Database provides textual summaries and graphical visualization via UCSC Genome Browser custom tracks.

Conclusions:

  • PLANdbAffy enhances the accuracy of gene expression analysis using Affymetrix microarrays.
  • The database aids researchers in selecting reliable probes and interpreting gene expression data.
  • Integration with genome browsers facilitates comprehensive data analysis.