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Analysis of Complex Networks by Frank Emmert-Streib, Matthias Dehmer

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11.3 Modeling Metabolic Pathway Mappings

A metabolic pathway is a series of chemical reactions catalyzed by enzymes that occur within a cell. Metabolic pathways are represented by directed networks in which vertices correspond to enzymes and there is a directed edge from one enzyme to another if the product of the reaction catalyzed by the first enzyme is a substrate of the reaction catalyzed by the second.

Mapping metabolic pathways should capture the similarities of enzymes represented by proteins as well as topological properties that cannot always be reduced to sequential reactions represented by paths. The commonly used measure of enzyme dissimilarity is the logarithm of the number of different enzymes in the lowest common upper class (see, e.g., [2, 6]).

A different approach (Cheng, Harrison, and Zelikovsky [14]) makes full use of the Enzyme Commission number (EC number) and the tight reaction property classified by EC. The EC number is expressed with a four-level hierarchical scheme. The 4-digit EC number, d1.d2.d3.d4, represents a subsubsubclass indication of a biochemical reaction. If d1.d2 of two enzymes are different, and their similarity score is infinite; if d3 of two enzymes are different, their similarity score is 10; if d4 of two enzymes are different, their similarity score is 1; or else the similarity score is 0. The corresponding penalty score for a gap is 0.5. Cheng, Harrison, and Zelikovsky's [14] experimental study indicates that the proposed similarity score ...

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