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These conclusions were drawn primarily from simulations in which the univariate distribution of simulated expression values was closely approximated by what might be expected for Affymetrix mRNA expression array data using a Robust Multi-array Average normalization approach.
We simulated expression levels of miRNAs for normal and tumor samples by controlling true differentially expressed miRNAs of tumor samples across all simulations.
Heat map of simulated construct outputs and simulated expression efficiency for long CDS.
Heat map of simulated construct outputs and simulated expression efficiency for short CDS.
Here we note that FGF expression is restricted to the apical ectodermal ridge (AER), and pF is therefore non-zero only on the distal boundary of the domain (dashed part of Fig. 2C; simulated expression patterns are shown in Fig. S1, S3G-J).
To visualize our approach, Figure S1 shows the simulated expression values of the top 12 genes ranked by the GTI.
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As it was mentioned above, the authors simulate expression data, including biological noise.
Gaussian noise was also added in order to simulate expression measurement error.
This property of an edge is given by the dynamical equations we used to simulate expression data.
We then simulate expression data for each tissue that conforms to the assumptions of our probability model for a specific choice of f and g, as follows.
It samples from known Saccharomyces cerevisiae and Escherichia coli networks to create sub-networks, for which it simulates expression data based on Michaelis-Menten and Hill kinetics.
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