- How large are the pathways you are looking at?
- Keep the hierarchy of pathways in mind:
- Some pathways occur in multiple other pathways, are all these processes likely to be affected?
- When multiple pathways are found, which higher level processes are they a part of?
- When the proteins you are interested in are in higher level pathways, are they constituents of one sub-process, or spread out over many sub-processes?
- Are the proteins you are interested in present in multiple pathways? Do they have a different set of interactors and/or function depending on the pathway?
- Keep in mind where the proteins are in the network
- How many of the proteins you are interested in are not annotated in the database?
- What are the scores for radiality and integration? In which categories would the proteins fall? If they are all isolated proteins, can you find out more about them?
- Are the proteins you are interested in close together in the network?
- Are the proteins you are interested in dependent on other proteins to form complexes to perform their functions in any of the pathways? Are those proteins present?
- Can you specify the proteoforms in your sample and use those to get more specific results?