Mining conserved neighborhood patterns in metabolic and genomic contexts

Abstract : This thesis fits within the field of systems biology and addresses a problem related to heterogeneous biological networks. It focuses on the relationship between metabolism and genomic context through a graph mining approach. It is well-known that succeeding enzymatic steps involving products of genes in close proximity on the chromosome translate an evolutionary advantage in maintaining this neighborhood relationship at both the metabolic and genomic levels. We therefore choose to focus on the detection of neighboring reactions being catalyzed by products of neighboring genes, where the notion of neighborhood may be modulated by allowing the omission of several reactions and/or genes. More specifically, the sought motifs are trails of reactions (meaning reaction sequences in which reactions may be repeated, but not the links between them). Such neighborhood motifs are referred to as metabolic and genomic patterns. In addition, we are also interested in detecting conserved metabolic and genomic patterns, meaning similar patterns across multiple species. Among the possible variations for a conserved pattern, the presence/absence of reactions and/or genes may be considered, or the different order of reactions and/or genes. A first development proposes algorithms and methods for the identification of conserved metabolic and genomic patterns. These methods are implemented in an open-source pipeline called CoMetGeNe (COnserved METabolic and GEnomic NEighborhoods). By means of this pipeline, we analyze a data set of 50 bacterial species, using data extracted from the KEGG knowledge base. A second development explores the detection of conserved patterns by taking into account the chemical similarity between reactions. This allows for the detection of a class of conserved metabolic modules in which neighboring genes are involved.
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https://tel.archives-ouvertes.fr/tel-01933663
Contributor : Alexandra Zaharia <>
Submitted on : Friday, November 23, 2018 - 9:02:09 PM
Last modification on : Wednesday, April 3, 2019 - 1:58:32 AM

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Alexandra Zaharia. Mining conserved neighborhood patterns in metabolic and genomic contexts. Bioinformatics [q-bio.QM]. Université Paris Saclay, 2018. English. ⟨NNT : 2018SACLS275⟩. ⟨tel-01933663v1⟩

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