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The toggle switch is controllable in the sense that the gap between the bistable states is adjustable as determined by the regulatory strength from the driver nodes.
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By incorporating the regulatory network information with the regulatory strength matrix, we have further inferred the activities and interactions between transcription factors and their target genes.
The regulatory strength of TF j onto target gene i is given by a randomly chosen coefficient -1 ≤ α ij ≤ 1.
The regulatory strength method is shown here to be topology-dependent.
Three methods for establishing and quantifying causal relationships between genes based on steady-state measurements in single-gene perturbation experiments have recently been proposed: the regulatory strength method, the local regulatory strength method, and Gardner's method.
However, they formed unmistakable clusters from the regulatory strength matrix, being linked to the regulatory influence of either STAT6 or MYC.
Based on the regulatory strength matrix, we have clustered the coexpressed and coregulated genes into different groups.
The regulatory strength matrix is clustered to determine gene groups which are not only co-expressed, but also co-regulated.
By assigning the parameters representing the regulatory strengths of the same edge into the one group, the group LASSO [ 10] can be applied to find the sparse network topology.
The regulatory strengths obtained by this method can also be used to compute local regulatory strengths.
In their method, the regulatory strengths between genes is assumed to be the same across all datasets.
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