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Blind source separation and the analysis of microarray data

Abstract : We develop an approach for the exploratory analysis of gene expression data, based upon blind source separation techniques. This approach exploits higher-order statistics to identify a linear model for (logarithms of) expression profiles, described as linear combinations of "independent sources." As a result, it yields "elementary expression patterns" (the "sources"), which may be interpreted as potential regulation pathways. Further analysis of the so-obtained sources show that they are generally characterized by a small number of specific coexpressed or antiexpressed genes. In addition, the projections of the expression profiles onto the estimated sources often provides significant clustering of conditions. The algorithm relies on a large number of runs of "independent component analysis" with random initializations, followed by a search of "consensus sources." It then provides estimates for independent sources, together with an assessment of their robustness. The results obtained on two datasets (namely, breast cancer data and Bacillus subtilis sulfur metabolism data) show that some of the obtained gene families correspond to well known families of coregulated genes, which validates the proposed approach.
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Submitted on : Tuesday, January 6, 2009 - 10:21:06 AM
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Pierre Chiappetta, Marie-Christine Roubaud, Bruno Torrésani. Blind source separation and the analysis of microarray data. Journal of Computational Biology, Mary Ann Liebert, 2004, 11 (6), pp.1090-1109. ⟨10.1089/cmb.2004.11.1090⟩. ⟨hal-00350129⟩



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