Classification of microarray data using gene networks

• Main Authors: Dutreix Marie, Zinovyev Andrei, Rapaport Franck, Barillot Emmanuel, Vert Jean-Philippe
• Format: Article
• Language: English
• Published: BMC 2007-02-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/8/35

<p>Abstract</p> <p>Background</p> <p>Microarrays have become extremely useful for analysing genetic phenomena, but establishing a relation between microarray analysis results (typically a list of genes) and their biological significance is often difficult. Currently, the standard approach is to map <it>a posteriori </it>the results onto gene networks in order to elucidate the functions perturbed at the level of pathways. However, integrating <it>a priori </it>knowledge of the gene networks could help in the statistical analysis of gene expression data and in their biological interpretation.</p> <p>Results</p> <p>We propose a method to integrate <it>a priori </it>the knowledge of a gene network in the analysis of gene expression data. The approach is based on the spectral decomposition of gene expression profiles with respect to the eigenfunctions of the graph, resulting in an attenuation of the high-frequency components of the expression profiles with respect to the topology of the graph. We show how to derive unsupervised and supervised classification algorithms of expression profiles, resulting in classifiers with biological relevance. We illustrate the method with the analysis of a set of expression profiles from irradiated and non-irradiated yeast strains.</p> <p>Conclusion</p> <p>Including <it>a priori </it>knowledge of a gene network for the analysis of gene expression data leads to good classification performance and improved interpretability of the results.</p>