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Every example in a set is placed as a positive example. Subdue runs on this example with the 10 iterations option. After phase 1, we can get a hierarchical tree of patterns. In the GDM phase 2 we can recover the erased names for the most interesting pattern of phase 1 to know its biochemical meaning. 2 Clustering in networks This experiments finds a common structure in every network in a species. The process follows the same way as the previous section. 4 shows the experimental set in clustering in networks.

The unnamed-graph representation of a biological network. edge is headed for the Entry, as a catalyst, from catalyzed the reaction. It is a general idea in biochemistry that the enzyme is considered as an assistant to the reaction even though it is almost always mandatory [52]. Relation shows the relationship between protein, gene, compound and map. The Relation node has several attributes. Two value vertices of Type and Subtype attributes are connected to the Relation vertex by a Type attribute edge and a Subtype attribute edge respectively.

A cell carries most of the processes for maintaining its life, because it is a functional and structural basic bio-organism by itself. The cell generates some energy from nutrients to maintain its life and reproduce. Also, it needs to protect itself against the outer environment and excrete garbages. Every activity of a cell is carried out as metabolism. Metabolism is a series of enzyme-catalyzed reactions that constitute metabolic pathways in a cell or organism [52]. Each consecutive reaction in a metabolic pathway makes a specific biochemical change.

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