Content | Edges in networks weighted by biological traits |
 | Overlays of protein-protein interactions and disease associations |
 | Overlays of protein-protein interactions and relevant pathways |
 | Distinctions between proteins and other molecules that might serve as mediators of interactions, e.g. enzymes |
 | Test statistics and counts (e.g. # of interactions, # of articles, overrepresentation of a functional term) and perceptually encoding nodes or links by them |
Interactivity | Updating of interactions (e.g. selection, color coding) across views – e.g. across overlaid networks |
 | Facile filtering (users had to use mini-scripting to filter) |
 | Facile color-coding (at the time it took 15+ steps to color code) |
 | Integrating one's own data into the displayed dataset |
 | Simplifying networks through zooming, filtering, color-coding, expanding some nodes but not others, mapping only select neighbors to pathways |
 | Conducting computations on networks to find e.g. shared paths to identify indirect interactions or recurrent or aberrant patterns that might signal a biologically significant set of relationships |
Workspaces | Spaces for comparing different networks side-by-side with dynamically linked interactions |
 | Spaces for aggregating entities on the fly into manipulable qualitative attributes based on emerging knowledge (e.g. normal vs disease conditions) |