Pathway preview

Overview

Pathway preview window generate visualization of pathways and help navigate and edit pathway related data. All features are available in popup menu by clicking the right button of the mouse in the window.

Search an existing pathway

The user can click "pathway selector" menu, and then a "pathway list" window is displayed. The user can choose one or more pathway from the list and click "add pathway" button. Then the graph of the selected pathways will be displayed in the "pathway preview" window.

Preview the pathway

The user may drag the scrollbars of the window to position the part of the pathway into the center of the window. By clicking "actual size", "zoom in" and "zoom out" menu, the size of the pathway graph can be changed. By clicking "bird eye" menu, the user can see a "pathway overview" window. The whole pathway will be visible in the "pathway overview" window and a red box is displayed in the window which matches the part of the pathway that is currently visible in the "pathway preview" window. The user can move or change the size of red box, then the visible part of pathway in "pathway preview" window will be change or zoomed.

All interactions and entities of the pathways will be displayed in the "pathway preview" window. User can preview the detail information of the interactions and entities by move the mouse over the box of the interaction or entity, then a window will be displayed to display the detail information.

Initially, the "pathway preview" window will display all components of the pathway. User can selectively hide some details in the preview. "hide genes" menu will hide all genes and transcriptions of the pathway. "hide genes and RNAs" will hide RNAs and translations of the pathway in addition to those of "hide genes". "metabolic network only" will hide proteins, composition relations, regulations in addition to those of "hide genes and RNAs".

Legends of the visual component in the pathway.

The color, shape and width of the boxes and lines follows the convention of FCModeler. For instances, red background means subcellular location "mitochondrion" or any subcategories of it; blue line means the catalysis function of the enzymes. Not all the conventions are supported in "pathway preview" window. For instance, all lines in the "pathway preview" window are straight lines

Search components of the pathway

To search components of the pathway, the user can click "search graph" menu. A dialog is displayed and the user can input entity name or interaction type. By clicking "apply" button, the component that matches the search criteria will be displayed in red color in the pathway preview window. All other components will be displayed in white color. User can quickly identify those components in "pathway overview" window and drag the red box in "pathway overview" window to move the pathway in "pathway preview" window. To restore the initial color legends in the "pathway preview" window, the user can click "apply metaphor" menu. If the graph in the "pathway preview" window is changed, user can reload the pathway by "reload pathway" menu and do not need select the pathway lists again.

Export graph of the pathway

Currently the program can export the pathway in PNG format picture without color. The user can export the current graph in the "pathway preview" window by clicking "export PNG" menu.

Edit components of the pathway

The user can choose any box or line in the "pathway preview" window, and then click "edit selection" menu. The program will determine the type of the selection and go to the "edit entity" window or "edit interaction" window correspondingly.

Merge two entities

See here.

PathBinder