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Figure 2 | BMC Systems Biology

Figure 2

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

Figure 2

Symbols of the modified Edinburgh Pathway Notation. Unique shapes and identifiers are used to distinguish between each element of the notation allowing its interpretation even in the absence of colour. Colour maybe used for aesthetic purposes and to ease identification of nodes. The notation can be broadly divided into four categories; components, boolean operators, transition nodes and annotated edges. Components consist of any interacting species from proteins, complexes, genes or other molecular species (pathogens, DNA, RNA). Pathway initiators are also presented in the notation. Boolean operators are essential for capturing the dependencies of an interaction. Transition nodes provide information as to the nature of the interaction (such as cleavage, translocation, phosphorylation). Edges are directional and can be coloured for visual impact. Distinctive arrow-heads are used to distinguish between the pathway inputs and outputs but are otherwise avoided. Instead in-line edge annotation is used to add a visual cue as to the meaning of an edge. Cellular compartmental information is provided by physical location and backdrop or by colouring nodes according to their sub-cellular location.

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