Error margin analysis for feature gene extraction

• Published in: BMC bioinformatics Vol. 11; no. 1; p. 241
• Main Authors: Chow, Chi Kin, Zhu, Hai Long, Lacy, Jessica, Kuo, Winston P
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 11.05.2010; BioMed Central; BMC
• Subjects: Algorithms; DNA microarrays; Gene expression; Gene Expression Profiling - methods; Genetic algorithms; Methodology article; Oligonucleotide Array Sequence Analysis - methods; Pattern Recognition, Automated - methods; United States; China
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-11-241

Feature gene extraction is a fundamental issue in microarray-based biomarker discovery. It is normally treated as an optimization problem of finding the best predictive feature genes that can effectively and stably discriminate distinct types of disease conditions, e.g. tumors and normals. Since gene microarray data normally involves thousands of genes at, tens or hundreds of samples, the gene extraction process may fall into local optimums if the gene set is optimized according to the maximization of classification accuracy of the classifier built from it. In this paper, we propose a novel gene extraction method of error margin analysis to optimize the feature genes. The proposed algorithm has been tested upon one synthetic dataset and two real microarray datasets. Meanwhile, it has been compared with five existing gene extraction algorithms on each dataset. On the synthetic dataset, the results show that the feature set extracted by our algorithm is the closest to the actual gene set. For the two real datasets, our algorithm is superior in terms of balancing the size and the validation accuracy of the resultant gene set when comparing to other algorithms. Because of its distinct features, error margin analysis method can stably extract the relevant feature genes from microarray data for high-performance classification.