Bioinformatics pp 363-377

Part of the Methods in Molecular Biology™ book series (MIMB, volume 453)

Combinatorial Optimization Models for Finding Genetic Signatures from Gene Expression Datasets

  • Regina Berretta
  • Wagner Costa
  • Pablo Moscato

Abstract

The aim of this chapter is to present combinatorial optimization models and techniques for the analysis of microarray datasets. The chapter illustrates the application of a novel objective function that guides the search for high-quality solutions for sequential ordering of expression profiles. The approach is unsupervised and a metaheuristic method (a memetic algorithm) is used to provide high-quality solutions. For the problem of selecting discriminative groups of genes, we used a supervised method that has provided good results in a variety of datasets. This chapter illustrates the application of these models in an Alzheimer's disease microarray dataset.

Key words:

Combinatorial optimization integer programming gene selection feature selection gene ordering microarray data analysis Alzheimer's disease. 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Regina Berretta
    • 1
  • Wagner Costa
    • 2
  • Pablo Moscato
    • 3
  1. 1.Centre of Bioinformatics, Biomarker Discovery and Information-Based MedicineThe University of NewcastleCallaghanAustralia
  2. 2.School of Electrical Engineering and Computer ScienceThe University of NewcastleCallaghanAustralia
  3. 3.ARC Centre of Excellence in Bioinformatics, and Centre of Bioinformatics, Biomarker Discovery and Information-Based MedicineThe University of NewcastleCallaghanAustralia

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