Figure 4.

The web-accessible pathway navigator. A sample pathway is shown that represents part of the viral activated signaling pathways in human dendritic immune cells. The entities and links shown in the pathway are clickable to display the corresponding annotations. The content of the individual frames, which are indicated by roman numerals, are as follows: I – Help link. II – brief author provided description of the pathway and contact information for suggesting pathway revisions. III – link for the pathway legend (from CellDesigner), and links for collated lists of the annotations for interactions, protein, genes, and RNAs in the network. IV.1 navigating zoom rectangle. Dragging the zoom rectangle or clicking inside the index window (IV.2) displays the appropriate section of the pathway in IV.3. The arrow in IV.1 is a toggle button to hide/unhide the index window. The zoom facilitates navigating, particularly when the network map is large and fine-grain. V, VII, VIII, IX – sorted, hyperlinked lists of all the interactions, proteins, genes and RNAs, respectively. Clicking on a hyperlink displays the annotations in the annotation frame (VI). Links to the Entrez gene pages and the appropriate page of a public wiki-based discussion forum also launch new windows. VI – annotation frame which displays selected annotations. Clicking an interaction displays the annotations. Clicking a PMID opens a separate PubMed window for that citation.