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Dandekar AG, Bioinfo, Uni Wuerzburg
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Boolean model

George Boole (*2.11.1815; 8.12.1864)

We give here the Boolean model for the combined intracellular interaction model in XML format. This can then be used for simulation of the whole network and its behaviour, for instance as detailed in the results applying SQUAD (di Cara et al., 2007).

File download

  model file : rp_interaction.xml

Analysis


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Figure 1. Network topology for the cell-cell interaction model. Apoptosis, proliferation and survival pathways belonging to the hepatocyte cell are shown on the top. Pathways for Kupffer cells are shown on the bottom with two interactions connecting both cell types. Method: The SBML was set up with Celldesigner Version 3.5.1 and analysed with SQUAD on a windows computer.



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Supplementary material

Network topology for apoptosis (top cascade), proliferation and survival in hepatocytes in the cell-cell interaction model. Snapshot for the switching state between proliferation/survival and apoptosis. The activation level ranges from white (completely inactive) to black (completely active).


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Supplementary figure 2


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SQUAD simulation of apoptosis in hepatocytes in the cell-cell interaction model. Activation values for network nodes are calculated and translated into concatenation predictions. Maximum value is 1, minimum value is 0. One time unit of the model (1.0 units) corresponds, according to the experimental data, to one day of hepatocytes in culture.



Supplementary Figure 3



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Hepatocyte apoptosis: Execution pathway model. Logical AND connections are represented by blue spheres. Activating arcs are represented by black arrows and inhibiting arcs by red lines with a bar. The influence of the housekeeping node is depicted in green color.



Supplementary Figure 4


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Combined pathways in one cellular model. The network map as it is also used for CNA is shown. It is divided in two parts to use it with CNA for lack of space and the maps are shown in parallel in two separate windows. Logical AND connections are represented by blue spheres. Activating arcs are represented by black arrows and inhibiting arcs by red lines with a bar. The influence of the housekeeping node is depicted in green color. The area of the detailed cell demise model is grey. The blue framed nodes are indicated on both maps for convenience.