Pathway and Network Explorer Toolbar

Pathway and Network Explorer Toolbar

The Pathway and Network Explorer toolbar, used to view analysis networks, My Pathways and Neighborhood Explorer, provides several key functions for examining network diagrams.

 

Button	Name and Function
	Save: Saves the current network diagram.
	Delete Selected: Removes selected (highlighted) molecules from the network diagram.
	Copy: Saves highlighted molecules to the clipboard.
	Paste: Returns molecules in the clipboard back to a network diagram.
	Undo: Reverses the last action.
	Redo: Repeats the last undone action.
	Add to List: Selected molecules can be added from a network, pathway, or neighborhood by clicking this icon.
	Open Right Click Menu: This icon is only available on Mac computers. It functions as a tool to open the menu that is available in Pathways, Networks, and Neighborhoods by right-clicking the mouse.
	Find Genes: Locates a gene within a network, neighborhood, or My Pathway. Once identified, the gene will be identified in blue.
	Full Screen View: Toggles to a full-screen view. Graph navigation tools are available to move around the network or pathway. Use Right click to exit from Full Screen view, or Esc.
	Auto-Layout: Redraws the network diagram with molecules laid out with even spacing.
	Toggle Subcellular Layout: Shifts the spatial location of molecules into their corresponding subcellular locations.
	View annotations: Gives details of all the selected molecules
	View/ Edit Preferences: Click to change the font sizes in network explorer. Changing the font size does not change the corresponding molecule size.
	Zoom Selected: Zooms in on selected area of window.
	Magnifying Lens: Use this tool to enlarge portions of pathways and networks. Click it, then hover with the mouse over the area you wish to see more detail.
	Refresh: Updates existing connections with the latest content from the Ingenuity Knowledge Base.
	Edit Notes: Allows you to change the notes on a saved Pathway or List.
	Open Report: Opens a Pathway or List report.
	Build: Opens a menu at the left of the screen for accessing Grow, Path Explorer, Connect, Trim, and Add Molecules/ Relationships.
	Overlay: Opens a menu at the left of the screen for overlaying Expression values, Functions and Diseases, Lists, Drugs, Canonical Pathways, and Custom Pathways and for Highlight and Species/ Tissue Highlight.
	Path Designer: Use Path Designer to transform your networks and pathways in IPA into publication quality pathway graphics rich with color, customized text and fonts, biological icons, organelles, and custom backdrops.
	Export Image: Export an image of your network up to 600 dpi.
	Export Data: Export a list of genes with associated identifiers, expression values and gene details.
	Print: Generates a hard copy of the network diagram.
	Email : Send interactive pathway to a colleague

 

Graph Navigation Tools

This tool is available from networks and pathways. The arrow keys allow you to move the network left, right, up, and down. The + button acts as a Zoom In tool. The "-" button is a Zoom Out tool. Clicking the circle in the center Fits the network to the screen.

 

Clicking the the double  arrow in the top left opens an overview of the network so that you can determine where on the page you are focusing.

 

Subcellular Layout

The Subcellular Layout View rearranges molecules into their various subcellular compartments: nucleus, cytoplasm, plasma membrane and extracellular space.  An unknown category also exists for molecules which no subcellular localization information is currently available.

 

Once Network Explorer is launched, click the Subcellular Layout button in the Network Explorer toolbar at the top of the window.

The cellular compartments are demarcated by solid black lines and labeled accordingly as shown below.

 

 

 

You can toggle Subcellular Layout View and return to the default display by clicking on the Subcellular Layout button once again.