ACoM: A classification method for elementary flux modes based on motif finding |
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Authors: | Pérès S Vallée F Beurton-Aimar M Mazat J P |
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Affiliation: | a LRI CNRS UMR 8623, Université Paris-Sud 11, 91405 Orsay Cedex, France b LABRI UMR 5800 - Université Bordeaux 1 351, cours de la Libération, 33405 Talence Cedex, France c INSERM U688 Université de Bordeaux 2, 146 rue Léo-Saignat, 33076 Bordeaux-Cedex, France |
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Abstract: | Elementary flux mode analysis is a powerful tool for the theoretical study of metabolic networks. However, when the networks are complex, the determination of elementary flux modes leads to combinatorial explosion of their number which prevents from drawing simple conclusions from their analysis. To deal with this problem we have developed a method based on the Agglomeration of Common Motifs (ACoM) for classifying elementary flux modes. We applied this algorithm to describe the decomposition into elementary flux modes of the central carbon metabolism in Bacillus subtilis and of the yeast mitochondrial energy metabolism. ACoM helps to give biological meaning to the different elementary flux modes and to the relatedness between reactions. ACoM, which can be viewed as a bi-clustering method, can be of general use for sets of vectors with values 0, +1 or −1. |
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Keywords: | Metabolic pathway analysis Elementary flux modes Classification Agglomerative algorithm for common motifs Mitochondrial energy metabolism |
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