An integrated algorithm for gene selection and classification applied to microarray data of ovarian cancer.
OBJECTIVE
The type of data in microarray provides unprecedented amount of data. A typical microarray data of ovarian cancer consists of the expressions of tens of thousands of genes on a genomic scale, and there is no systematic procedure to analyze this information instantaneously. To avoid higher computational complexity, it needs to select the most likely differentially expressed gene markers to explain the effects of ovarian cancer. Traditionally, gene markers are selected by ranking genes according to statistics or machine learning algorithms. In this paper, an integrated algorithm is derived for gene selection and classification in microarray data of ovarian cancer.


METHODS
First, regression analysis is applied to find target genes. Genetic algorithm (GA), particle swarm optimization (PSO), support vector machine (SVM), and analysis of variance (ANOVA) are hybridized to select gene markers from target genes. Finally, the improved fuzzy model is applied to classify cancer tissues.


RESULTS
The microarray data of ovarian cancer, obtained from China Medical University Hospital, is used to test the performance of the proposed algorithm. In simulation, 200 target genes are obtained after regression analysis and six gene markers are selected from the hybrid process of GA, PCO, SVM and ANOVA. Additionally, these gene markers are used to classify cancer tissues.


CONCLUSIONS
The proposed algorithm can be used to analyze gene expressions and has superior performance in microarray data of ovarian cancer, and it can be performed on other studies for cancer diagnosis.
Lee
Zne-Jung
ZJ
Department of Information Management, Huafan University, Shihding Township, Taipei County 22301, Taiwan, ROC. johnlee@hfu.edu.tw
D000465:Algorithms; D003198:Computer Simulation; D005260:Female; D017143:Fuzzy Logic; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010051:Ovarian Neoplasms / Q000235:genetics / Q000378:metabolism*; D010363:Pattern Recognition, Automated / Q000379:methods; D012044:Regression Analysis