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The inferred network consists of 36 modules of average size 17.5 genes (±19.7 genes), 11 with a single regulator and 4 with two regulators, with regulation paths of average length of 2.5.
Finally, a last model for the flagella system was tested in which the time delay affects both the expressions for FA and FL, model FF.C1.OR.3: (22) In an incoherent FF motif, the two regulation paths flowing from the master regulator display opposite signs.
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PMN may miss a true regulator if a full regulation path is missing (hurting recall), the reconstructed pathways are sensitive to noise in the interaction measurements, and certain types of interactions (protein modifications, chromatin occupancy, cellular localization), as well as alternative splicing, are not modeled in the simple interaction graph.
A PMN 𝒫=〈ℳ,ℐ〉 model has a consistent configuration if each regulator in the Module Network has a regulation path from its protein to the genes in its target module (Fig. 2).
But this regulation path still remains to be shown using genetic models.
The shortest regulation path could be obtained by tracing back the process.
The algorithm returned the shortest regulation path between a given TF-gene pair in the regulatory relation network.
In PEIIA Glc &cAMP subpathway (includes actions labeled S1, S2, S3, G1.1, G1.2, G3 ), regulations S1 and S2 are shared with the other two regulation path-ways.
The regulation path is partially directed, such that the edge between vℓ and vℓ+1 is either undirected or directed from vℓ to vℓ+1.
The 'coherent' means the sign of the direct regulation path from the transcription factor to the dependent gene is the same as the overall sign of the indirect regulation path from the transcription factor through the co-transcription factor to the dependent gene in Figure 7(b).
Therefore, when a regulation path does not work for some proteins, the system will assign other paths to process regulations in order to avoid the overall collapse caused by a small portion of damage.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com