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Unlike other techniques, DSM can create a dependency matrix without relying on mapping higher level components.
The information how the species influence each other can be stored in a compact manner in a dependency matrix[ 10].
The shortest positive or negative paths among pairs of nodes can be used to determine a dependency matrix [ 10, 11, 32, 35] which reflects the long-range regulatory relationships among signaling components.
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We separately version the components and interfaces based on a Component-Interface Dependency Matrix (CIDM), and analyze impacts according to their dependency relationship.
Note also that the initial response of ERK to a stimulation with EGF was positive, as correctly predicted by the dependency matrix (see Figure 3; EGF is a weak activator of ERK) and by the initial response prediction in the logical model when switching off the negative feedback loop (by cutting the edge from ERK to SOS).
This work applies a dependency structure matrix to identify design dependencies.
Nevertheless, this explanation cannot be accepted out of hand: the dependency matrix reveals that RGT1 is an ambivalent factor with regard to SNF3, i.e., both repressing and activating paths from RGT1 to SNF3 exist.
A major difference to the previously described approach using the dependency matrix is that, in the latter, all experimental observations are treated independently, while here, the response of several readouts measured in the same experiment must be consistent to each other.
The dependency matrix thus summarizes information on network topology in a very condensed way.
For example, after increasing the expression level of ErbB2, an increase in MEK phosphorylation and a decrease in ERK phosphorylation are both in accordance with the dependency matrix given in Figure 3.
There are several ways to represent precedence graph: dependency matrix, sparse matrix representations, graph traversal algorithms, and topological sorts.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com