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Figure 4 | BMC Systems Biology

Figure 4

From: A logic-based diagram of signalling pathways central to macrophage activation

Figure 4

Automated layouts of the pathway diagram. (4a) a hierarchical-classic layout was applied to the entire pathway and the orientation was set to flow from left to right. Nodes are coloured according to their sub-cellular location. With this layout the flow of pathway information and biological logic is maintained, such that the inputs to pathway are placed at the left side of the diagram and these can be followed through to the outputs at the right hand side. (4b) a detailed inset of the hierarchical-classic layout of the integrated pathway taken from 4a. (4c) Organic-classic automated layout of the entire pathway generated in yEd graph editor. Although the directionality of flow in the pathway is lost, interacting partners tend to be placed in close proximity of each other in this layout. (4d) a 3-dimentional network of the apoptosis interactions in the pathway generated using BioLayout Express3D. This network can be queried for pathway information. Unique shapes are used to identify the different pathway notation symbols; spheres denote interacting components (proteins, genes, complexes), decahedron shapes represent boolean operators or transition nodes and tetrahedron shapes correspond to the in-line edge annotation (in this case activation, or inhibition). All notation symbols are coloured to correspond to the colour scheme applied in the 2-dimentional pathway diagram (e.g. complexes are yellow, proteins are blue, and activation-annotations are green). Furthermore interacting components are sized according to type, such that spheres representing complexes appear larger than proteins or genes. As with the 2-dimentional diagram the colour scheme used is customisable. The 3-dimentional network retains the information captured in the 2-dimentional pathway and although spatial placement of nodes in relation to their sub-cellular location has been lost, this information can be retrieved by querying the network and/or colouring nodes according to their sub-cellular location.

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