Cluster analysis of genome-wide expression data for feature extraction

Authors:
Kuo-Sheng Lin;Chen-Fu Chien
Affiliations:
Department of Industrial Engineering and Engineering Management, National Tsing Hua University, 101 Section 2 Kuang Fu Road, Hsinchu 30013, Taiwan, ROC;Department of Industrial Engineering and Engineering Management, National Tsing Hua University, 101 Section 2 Kuang Fu Road, Hsinchu 30013, Taiwan, ROC
Venue:
Expert Systems with Applications: An International Journal
Year:
2009

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Abstract

Bio-chip data that consists of high-dimensional attributes have more attributes than specimens. Thus, it is difficult to obtain covariance matrix from tens thousands of genes within a number of samples. Feature selection and extraction is critical to remove noisy features and reduce the dimensionality in microarray analysis. This study aims to fill the gap by developing a data mining framework with a proposed algorithm for cluster analysis of gene expression data, in which coefficient correlation is employed to arrange genes. Indeed, cluster analysis of microarray data can find coherent patterns of gene expression. The output is displayed as table list for convenient survey. We adopt the breast cancer microarray dataset to demonstrate practical viability of this approach.