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Molecules and reactions annotated within PathoPlant can be visualized as signaling pathway maps. A map of all reactions and respective molecules annotated to PathoPlant is generated by selecting 'Complete map' from the 'Signaling pathways' menu. Different types of polygons represent different types of molecules that are connected by arrows representing the signaling pathway reaction. Arrow types and colors represent different reaction categories given by the legend.
Within the map, an arrow can be selected in order to obtain detailed information on a particular reaction and the molecules involved. A molecule from the map can also be selected to obtain a partial specific pathway map starting from the selected molecule including reactions and molecules two pathway levels upstream and downstream of the molecule. Such a specific pathway map can also be generated by selecting 'Specific map' from the 'Signaling pathways' menu that in the first instance categorizes all molecules annotated PathoPlant with respect to the molecular function represented by different types of polygons. A category can subsequently be selected in order to display all molecules matching this category. By selecting 'Draw map' from this results list, a partial specific pathway map will be generated starting from the selected molecule including reactions and molecules two pathway levels upstream and downstream of the molecule.
By selecting 'Ethylene' from the 'Signaling pathways' menu, a hand-drawn map of the well-characterized Arabidopsis thaliana signaling pathway will be displayed. Individual molecules and reactions can be selected to obtain detailed information on the respective molecules or reactions.

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