Functional Coherence of Molecular Networks in Bioinformatics by Mehmet Koyutürk download in pdf, ePub, iPad
Biopathways and protein interaction databases. This can be easily enforced by ensuring that each branch in the hierarchy is represented by at most one term in each set. An example is a bias introduced by collecting more data in parts of networks that are relevant for human disease due to increased interest and availability of funding.
Indeed, global network representation of metabolic networks enables the study of metabolic network dynamics from a systems perspective. Flannick, Eduardo Abeliuk, Antal F.
For this reason, we want our network comparison methods intentionally to be more flexible, or approximate. In this paper, we generalize and extend our results to quantify the functional coherence or similarity of a set of biomolecules as opposed to a pair. We also apply the measures to randomly generated groups and identify measures that induce the greatest separation between the test and random groups. Hence, we must rely on approximate solutions resulting from heuristic algorithms. Functional coherence in domain interaction networks.
Clearly, the spoke model introduces fewer false positives than the matrix model, but it can miss true interactions. Modular organization of cellular networks.
Organizing and computing metabolic pathway data in terms of binary relations. Inferring functional information from domain co-evolution. The field is likely to stay at the forefront of scientific research in the years to come. The two subsequent chapters focus on functional evolution of molecular networks. In such a model, enzymes correspond to nodes of the graph and a directed edge from one enzyme to another indicates that a product of the first enzyme is a substrate of the second.
Inferring protein domain interactions from databases of interacting proteins. Without loss of generality, we refer to concepts as terms throughout this paper. The degree of a node is the number of edges that the node touches. Papin, Tony Hunter, Bernhard O. Consequently annotations of molecules correspond to sets of terms, as opposed to individual terms.
Let Gc be the set of molecules associated with term c in the available database, with Gr being the set of all molecules. These methods use principles that are supported by various lines of empirical evidence. For example, in the network presented in Fig. Based on such comparisons, network models have been proposed for cellular and other real networks if their properties fit the properties of cellular networks Sect. The field of computational and systems T.
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