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NetworkBLAST-M progressively constructs a layered alignment graph, with each layer corresponding to a network.
Significance of changes in expression in pathways or networks is evaluated in the MetaCore™ suite based on the size of the overlap between user's dataset and a set of genes corresponding to a network or pathway queried.
The significance of changes in expression in pathways or networks is based on the degree of overlap between the user's dataset and a set of genes corresponding to a network or pathway queried.
Significance (p-values) in GeneGo of a biological pathway is evaluated based on the size of the intersection between user's dataset and set of genes/proteins corresponding to a network module/pathway in question.
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We discuss first the behavior of networks corresponding to A and D configurations (the synthetic classes of the empirical email and PGP networks, respectively).
Instead of selecting a specific tuning parameter corresponding to a determinant network topology, an adapted stability selection procedure is used to lead to a network consisting of edges with scores.
This could be formalized by unwrapped network[22] corresponding to a loopy network.
Thus the number of state space graphs corresponding to a single network may be as large as 2r.
Our model reduction method involves rewriting of the complex graph corresponding to a given network.
The range of the r-values is between +1 and - 1, r < 0 corresponding to a disassortative network whereas r > 0 to an assortative one.
Here, we are interested in those flux distributions that maximize a predefined objective corresponding to a metabolic network function, such as growth or product yield.
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