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Analyzing Metabolic Networks: Topological Features and Genomic Insights

Explore metabolic network topology characteristics and integrate genomic data to predict essentiality of reactions using machine learning. Understand local topology, choke points, and reaction profiles.

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Analyzing Metabolic Networks: Topological Features and Genomic Insights

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  1. Metabolic Network 1) Topology based features • Local topology • Deviations • Choke and load points • Damages 2) Genomic and transcriptomic data ATCGAGTTGCAAT ATAGAA – TGCA-T - Gene expression - Homologous genes reaction 3) Flux balance analysis metabolite - Biomass objective flux Feature creation Features Essentiality classes NNNR PUP NNR NP NS RUP CCV . . . E: Essential 1 E N N: Non-essential N Reactions . . . . . . i 1 4 E 3 . . . . . . i Reaction profile The machine learning system (SVM)  Essential o Trained classifier o o o o o x x o x o x Prediction for the reaction to be essential Non-essential x o x o o Input space Space of the kernel x x o x x

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