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Related Experiment Videos

An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments.

R S Anderssen1, Y Wu, R Dolferus

  • 1CSIRO Mathematical and Information Sciences, GPO Box 664, Canberra ACT 2601, Australia. Bob.Anderssen@csiro.au

Bioinformatics (Oxford, England)
|February 28, 2004
PubMed
Summary

To improve gene discovery, a new sampling strategy prioritizes sequencing clones with lower fluorescence intensities from cDNA microarrays. This method reduces redundancy and enhances the identification of novel genes from anonymous libraries.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Gene discovery often relies on anonymous cDNA microarrays due to sequencing costs.
  • These arrays contain redundant clones proportional to gene expression levels.
  • Redundancy in identified clones complicates subsequent sequencing and gene discovery.

Purpose of the Study:

  • To propose an a posteriori sampling strategy to enhance gene discovery from cDNA microarray experiments.
  • To reduce the impact of clone redundancy in identified pools.
  • To optimize the selection of clones for sequencing.

Main Methods:

  • Developed a strategy prioritizing clones with lower fluorescence intensities.
  • Formalized the assessment of fluorescence intensity for spot selection.

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  • Validated the method using actual microarray data with known clone sequences.
  • Introduced and utilized repeat plots for visualizing fluorescence intensity measures.

    • Main Results:

    • Sequencing clones with lower fluorescence intensities preferentially reduces redundancy.
    • This strategy enhances the opportunity for gene discovery compared to random sequencing.
    • Avoiding pooling of different biological libraries and focusing on low-intensity clones is beneficial.

    Conclusions:

    • The proposed sampling strategy effectively enhances gene discovery from cDNA microarrays.
    • Prioritizing low-intensity clones is a more efficient approach than random selection.
    • Optimizing clone selection based on fluorescence intensity is crucial for cost-effective gene discovery.