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.