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Pathway Interaction Database homepage

Network maps

The graphics are interactive in each of Joint Photographic Experts Group (JPG), Scalable Vector Graphics (SVG) and Silverlight formats allowing users to click on items in the predefined pathways or dynamically generated network maps for further information. Network maps are displayed in JPG format by default. See the Output formats page for more information about the different formats and installing web browser plug-ins where necessary.

Navigating a JPG image

Use the browser scroll bars to navigate the image, and click on each object to gain additional information on the biomolecule or interaction. JPG does not offer zooming or panning capabilities.

Navigating an SVG image

Use the left mouse button to activate the image. Click on each object to gain additional information on the biomolecule or interaction.

Zooming: Use the right mouse button and select 'Zoom In' or 'Zoom Out'. Alternatively, hold the control (ctrl) key and left-click to zoom in at the mouse pointer location. Hold the ctrl key and click-and-drag to select a region to zoom into. Hold the ctrl and shift keys and click to zoom out.

Panning: Hold down the alt key and click-and-drag with the mouse to pan across the image.

For more information, right click the mouse on the image and select the 'Help' option.

Navigating a Silverlight image

Zoom is available at the top-left of the image.

To pan merely drag the image with the mouse.

Within the image you may search for specific molecules or all molecules at a certain subcellular location. To search for molecules you may enter their names, Entrez Gene identifiers or UniProt accession numbers.

Features of a Network map in JPG, SVG and Silverlight formats:

A typical network map is shown below:

Figure 1

In this case, a predefined pathway is shown along with information about the pathway revision date, data source and so on. This pathway-specific information is not shown on network maps generated dynamically from search results, but in other respects both types of network displays are identical.

Predefined pathways as well as dynamic network map pages provide the option to toggle between JPG, SVG and Silverlight graphic formats by clicking on appropriate buttons on these pages. The option to view the network map code as PID XML or BioPAX is also provided. See Output formats for more information about the different formats.

The biomolecules and references used for a particular pathway can be viewed and downloaded from the network map pages by clicking on the appropriate buttons.

The graphic shows various elements of the network:

When a network map is generated to display the results of a search in which upstream and downstream interactions are included, then the upstream and downstream biological events are colored brown.

A predefined pathway can link to pathway subnetworks, and other predefined pathways. These links will appear as gray boxes with the network name within the box.

When two or more members of a biomolecular family are used in a network, this will be indicated by linking them to a family name via dotted maroon lines. Clicking on the family name will open a list of the family members.

A key to the iconography is provided at the bottom of each web page containing network maps: Figure 2

Molecule Use page

Clicking on a biomolecule in a network map will open the Molecule Use page, which provides context-specific details on the biomolecule within the network map. The Molecule Use page provides information on, for example, the biomolecule's role, activity state or post-translational modification(s).

Figure 3

Molecule Page

Clicking on the 'View the biomolecule Molecule Page for more information' link in the Molecule Use page opens a Molecule Page that contains all information on that biomolecule stored within the database, including the biomolecule's involvement in complexes and pathways.

Users can also access Molecule Pages from the PID Search results summary page and the Entrez Gene Linkout section.

Depending on the type of biomolecule, the Molecule Pages may vary slightly.

a) Molecule Page for a protein, compound, or RNA:

Both the Molecule Use Page and Molecule Page for proteins, compounds or RNAs contain information such as additional biomolecule names, external identifiers, and an internal PID identifier. Additionally, the Molecule Page lists the biomolecule's involvement in complexes and pathways within the database. Duplicate names in the complex list indicate physical properties differences among the complex constituents.

Figure 4

b) Molecule Page for a complex

Both the Molecule Use Page and Molecule Page for a complex contain an internal PID identifier, and a Gene Ontology (GO) identifier when available. The Molecule Page also lists the complex constituents and their subcellular locations, activity states and post-translational modifications. The Molecule Page also shows the complex's involvement in pathways in the database.

Figure 5

c) Molecule Page for a biomolecular family

The Molecule Use page will indicate if a biomolecule is part of a family. Clicking on the family name will open the Molecule Page for the family, which lists the family members, and the family's involvement in complexes and pathways.

Figure 6

Figure 7

d) Molecule Page for a cleaved protein

The Molecule Use page will indicate if a protein has been cleaved into one or more subunits and provides a link to the cleaved subunit's Molecule Page. This page lists the parent protein external identifier, a subunit specific internal PID identifier, and the subunit cleavage coordinates (included in parenthesis next to the subunit name).

Figure 8

Figure 9

Interaction Page

Clicking on a biological event in a network map will open the Interaction Page, which lists the source of data, constituent biomolecules, their roles, and pathways containing the interaction. The interaction can also be displayed graphically by clicking on the JPG or SVG options. From the graphic interaction page the user can sequentially add color-coded upstream and downstream interactions.

Figure 10

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