Robust gene signatures from microarray data using genetic algorithms enriched with biological pathway keywords.
Genetic algorithms are widely used in the estimation of expression profiles from microarrays data. However, these techniques are unable to produce stable and robust solutions suitable to use in clinical and biomedical studies. This paper presents a novel two-stage evolutionary strategy for gene feature selection combining the genetic algorithm with biological information extracted from the KEGG database. A comparative study is carried out over public data from three different types of cancer (leukemia, lung cancer and prostate cancer). Even though the analyses only use features having KEGG information, the results demonstrate that this two-stage evolutionary strategy increased the consistency, robustness and accuracy of a blind discrimination among relapsed and healthy individuals. Therefore, this approach could facilitate the definition of gene signatures for the clinical prognosis and diagnostic of cancer diseases in a near future. Additionally, it could also be used for biological knowledge discovery about the studied disease.
Departmento de Lenguajes y Ciencias de la Computación, University of Málaga, Bulevar Louis Pasteur, 35, 29071 Málaga, Spain. Electronic address: rmluque@lcc.uma.es.
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Luque-Baena
Departmento de Lenguajes y Ciencias de la Computación, University of Málaga, Bulevar Louis Pasteur, 35, 29071 Málaga, Spain; Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain. Electronic address: durda@lcc.uma.es.
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Urda
Supercomputing and Bioinformatics Centre, University of Málaga, C/ Severo Ochoa, 34, 29590 Málaga, Spain. Electronic address: claros@uma.es.
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Gonzalo Claros
Departmento de Lenguajes y Ciencias de la Computación, University of Málaga, Bulevar Louis Pasteur, 35, 29071 Málaga, Spain; Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain. Electronic address: lfranco@lcc.uma.es.
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Franco
Departmento de Lenguajes y Ciencias de la Computación, University of Málaga, Bulevar Louis Pasteur, 35, 29071 Málaga, Spain; Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain. Electronic address: jja@lcc.uma.es.
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Jerez
D000465:Algorithms; D030541:Databases, Genetic; D006801:Humans; D007938:Leukemia / Q000235:genetics / Q000473:pathology; D008175:Lung Neoplasms / Q000235:genetics / Q000473:pathology; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D011471:Prostatic Neoplasms / Q000235:genetics / Q000473:pathology
Biological enrichment; DNA analysis; Evolutionary algorithms; Feature selection