Pattern Discovery in Gene Expression Data

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Author(s): Gráinne Kerr (Dublin City University, Ireland), Heather Ruskin (Dublin City University, Ireland)and Martin Crane (Dublin City University, Ireland)
Copyright: 2009
Pages: 20
Source title: Intelligent Data Analysis: Developing New Methodologies Through Pattern Discovery and Recovery
Source Author(s)/Editor(s): Hsiao-Fan Wang (National Tsing Hua University, ROC)
DOI: 10.4018/978-1-59904-982-3.ch003

Keywords: Data Mining and Databases / Information Science Reference / Knowledge Discovery / Library & Information Science

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Abstract

Microarray technology1 provides an opportunity to monitor mRNA levels of expression of thousands of genes simultaneously in a single experiment. The enormous amount of data produced by this high throughput approach presents a challenge for data analysis: to extract meaningful patterns, to evaluate its quality, and to interpret the results. The most commonly used method of identifying such patterns is cluster analysis. Common and sufficient approaches to many data-mining problems, for example, Hierarchical, K-means, do not address well the properties of “typical” gene expression data and fail, in significant ways, to account for its profile. This chapter clarifies some of the issues and provides a framework to evaluate clustering in gene expression analysis. Methods are categorised explicitly in the context of application to data of this type, providing a basis for reverse engineering of gene regulation networks. Finally, areas for possible future development are highlighted.

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