Using menu
- Pathway diagram can be visualized at three scales
- FULL - with all details, as it appears in CellDesigner file,
- compact - the map is scaled at 60% of the full size, some details such as complex names and residue names are hidden for clarity
- tiny - scaled at 30% of the full size
- Modular view presents more abstract description of RB/E2F pathway at the level of modules identified and their relations
- All entities opens in the right 'info' panel the list of all entities present in the pathway.
In the list there is a distinction made between proteins and genes.
- List of modules opens in the right 'info' panel the list of 24 modules into which the pathway is separated.
Accessing pathway information
- To find the part of the diagram related to a protein, or a gene regulated by the RB/E2F pathway, the user can use
the 'all entities' list in the 'info' panel. The standard searching browser function can be utilized in the frame.
- Every entity page contains a list of links to the pages of chemical species associated with this entity.
When opening a chemical species page, the user has possibility to center the pathway map on this species by clicking
on 'center map' button.
- Every entity page contains links to the pathways in Broad's MSigDB database and to NetPath database in which the entity name
is identified.
- A chemical species or a reaction can be identified visually on the graphical image of the diagram.
When browsing the image map by mouse, the name of the species is simultaneously displayed in the 'top' panel (Element label).
- The user can zoom in and out the diagram by clicking on 'FULL', 'compact' or 'tiny' links
in the 'top' frame of the interactive diagram.
- For technical reasons, all reactions and species on the diagram are clickable but the 'catalysis' links are not clickable.
To find the description of the regulation through catalysis, the user should find the corresponding reaction and read the regulation
from it.
- The format of the textual reaction description is the following: A+B-C -> D+A. The 'minus' sign designates the fact that C acts as a catalyst (it is not consumed).
There are several other types of reactions. A@nucleus-t->A@cytoplasm designates transport 'pseudo' reaction.
A-?->B designates unknown transitions. A-->B designates transcriptional activation and A--|B transcriptional inhibition.
- To determine the transcriptional regulators of a gene, it is sufficient to click on it. The 'info' frame on the right will show
the list of the regulators. It is more preferable method to trying to find a specific dashed line connecting the gene to its regulators,
because the dashed lines often overlap. Similar is true for finding all reactions regulated by a catalyst.
Visualizing RB/E2F modules
- The module information can be accessed through 'modular view' or 'list of modules' command in the 'top' panel.
- Module can be visualized in two ways by clicking on 'CellDesigner' and 'Cytoscape' links. For CellDesigner module
visualization, the module layout corresponds to that of the full map.
- Zooming function is also applicable for module visualization. The desired visualization scale should be first chosen
by clicking on 'FULL', 'compact' or 'tiny' links in the top menu panel. After all module images will have the corresponding scale.
- For the Cytoscape notation of the modules image, see the BiNoM manual.