Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Genomic Tree of Gene Contents Based on Functional Groups of KEGG Orthology

  • Kim Jin-Sik (Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology) ;
  • Lee Sang-Yup (Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Department of BioSystems, BioProcess Engineering Research Center and Bioinformatics Research Center, Korea Advanced Institute of Science and Technology)
  • Published : 2006.05.01
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Abstract

We propose a genome-scale clustering approach to identify whole genome relationships using the functional groups given by the Kyoto Encyclopedia of Genes and Genomes Orthology (KO) database. The metabolic capabilities of each organism were defined by the number of genes in each functional category. The archaeal, bacterial, and eukaryotic genomes were compared by simultaneously applying a two-step clustering method, comprised of a self-organizing tree algorithm followed by unsupervised hierarchical clustering. The clustering results were consistent with various phenotypic characteristics of the organisms analyzed and, additionally, showed a different aspect of the relationship between genomes that have previously been established through rRNA-based comparisons. The proposed approach to collect and cluster the metabolic functional capabilities of organisms should make it a useful tool in predicting relationships among organisms.

Keywords

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