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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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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Probe mapping across multiple microarray platforms.

Jeffrey D Allen1, Siling Wang, Min Chen

  • 1UT Southwestern Medical Center, Dallas, TX 75390, USA.

Briefings in Bioinformatics
|December 27, 2011
PubMed
Summary
This summary is machine-generated.

Probe mapping is essential for integrating gene expression data from different microarray platforms. Combining BLAST alignment with vendor and Bioconductor annotations offers the most consistent cross-platform expression measurement.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Gene expression data analysis is increasingly complex due to the need for data integration across diverse microarray platforms.
  • Accurate probe mapping is a critical prerequisite for successful cross-platform data integration.
  • Existing probe mapping methods may not provide optimal consistency for integrating data from different vendors.

Purpose of the Study:

  • To systematically review and compare different probe mapping approaches across seven major microarray platforms from Affymetrix, Illumina, and Agilent.
  • To evaluate the consistency of expression measurements across platforms using empirical data.
  • To develop and provide tools for facilitating cross-platform microarray data integration.

Main Methods:

  • Systematic review and comparison of probe mapping strategies.
  • Utilized a unique dataset of 56 lung cancer cell line samples measured on two different microarray platforms.
  • Evaluated probe mapping accuracy using BLAST alignment against the Transcriptome, vendor annotations, and Bioconductor's Annotate package.

Main Results:

  • BLAST alignment of probe sequences to the Transcriptome outperformed vendor-provided annotations and Bioconductor's Annotate package.
  • A combined approach, termed 'Consensus Annotation' (integrating all three methods), yielded the most consistent expression measurements across platforms.
  • Empirical evaluation demonstrated the superiority of the Consensus Annotation method for cross-platform data integration.

Conclusions:

  • The Consensus Annotation method provides the most reliable probe mapping for integrating gene expression data across different microarray platforms.
  • Developed user-friendly web tools, an API, and an R package to aid researchers in cross-platform microarray data mapping.
  • These tools aim to simplify and enhance the integration of gene expression data from Affymetrix, Illumina, and Agilent platforms.