0000000000247759

AUTHOR

Ludovica Montanucci

showing 4 related works from this author

Additional file 1: of Gene connectivity and enzyme evolution in the human metabolic network

2019

Figure S1. Reaction graph generated from the human metabolic network reconstruction Recon3D. Figure S2. Distribution of the selection estimates calculated for genes with 1:1 orthologs in the 6 species (Human, Chimpanzee, Gorilla, Orangutan, Mouse, and Rat) in the global metabolic network. Figure S3. Correlation matrices between variables. Figure S4. Relationship between selection estimates and connectivity (degree, in-degree and out-degree) in the global metabolic network. Figure S5. Relationship between selection estimates and position. Figure S6. Number of genes under positive selection in each functional pathway of the global metabolic network. Figure S7. Distribution of the number of en…

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Gene connectivity and enzyme evolution in the human metabolic network

2019

[Background] Determining the factors involved in the likelihood of a gene being under adaptive selection is still a challenging goal in Evolutionary Biology. Here, we perform an evolutionary analysis of the human metabolic genes to explore the associations between network structure and the presence and strength of natural selection in the genes whose products are involved in metabolism. Purifying and positive selection are estimated at interspecific (among mammals) and intraspecific (among human populations) levels, and the connections between enzymatic reactions are differentiated between incoming (in-degree) and outgoing (out-degree) links.

ImmunologyPopulationMetabolic networkComputational biologyBiologyGeneral Biochemistry Genetics and Molecular BiologyEvolution Molecular03 medical and health sciencesNegative selectionDegreePurifying selectionAnimalsHumansSelection Geneticeducationlcsh:QH301-705.5GeneEcology Evolution Behavior and Systematics030304 developmental biologyMammalschemistry.chemical_classification0303 health scienceseducation.field_of_studyConnectivityNatural selectionNetwork topologyResearchApplied Mathematics030302 biochemistry & molecular biologyEnzymesPositive selectionFixation (population genetics)EnzymeMetabolismlcsh:Biology (General)chemistryModeling and SimulationGeneral Agricultural and Biological SciencesSelective sweepMetabolic Networks and Pathways
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Influence of pathway topology and functional class on the molecular evolution of human metabolic genes

2018

Metabolic networks comprise thousands of enzymatic reactions functioning in a controlled manner and have been shaped by natural selection. Thanks to the genome data, the footprints of adaptive (positive) selection are detectable, and the strength of purifying selection can be measured. This has made possible to know where, in the metabolic network, adaptive selection has acted and where purifying selection is more or less strong and efficient. We have carried out a comprehensive molecular evolutionary study of all the genes involved in the human metabolism. We investigated the type and strength of the selective pressures that acted on the enzyme-coding genes belonging to metabolic pathways …

0301 basic medicineComputer and Information SciencesEvolutionary ProcessesScienceMetabolic networkMetabolic networksBiologyTopologyGenomeBiochemistryEvolutionary geneticsEvolution Molecular03 medical and health sciencesNegative selection0302 clinical medicineMolecular evolutionEnzyme metabolismAnimalsHumansCentralityEnzyme ChemistryGeneSelection (genetic algorithm)030304 developmental biologyMammals0303 health sciencesEvolutionary BiologyMultidisciplinaryNatural selectionQRBiology and Life SciencesProteinsEvolutionary rateEnzymesMetabolic pathway030104 developmental biologyMetabolismMetabolic pathwaysEnzymologyMedicineMolecular evolution030217 neurology & neurosurgeryNetwork AnalysisResearch Article
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Additional file 2: of Gene connectivity and enzyme evolution in the human metabolic network

2019

Table S1. Reaction graph. List of edges of the directed reaction graph generated formed by the giant connected component of Recon3D. Table S2. Genes under positive selection in the global metabolic network. Table S3. Genes under recent positive selection in individual metabolic pathways. Table S4. Connectivity of metabolic genes under positive selection compared to the rest of metabolic genes in individual metabolic pathways. Table S5. Global metabolic network giant connected component gene/reaction information. Table S6. Individual metabolic pathways gene/reaction information. (XLSX 4140 kb)

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