Comments (2)
Here are the steps of the current workflow, with comments:
- Import full string network for HPV16 via "Import network from public database>String protein", select HPV16 and "all proteins of this species" => HPV16 is no longer an option in this interface
- Expand network with human interactors (10) using "Apps>String>Expand network" => Can't do this since we don't have an HPV network.
- Add specific host proteins
- Repeat network import/expansion for HPV1a => same problem as before
- Merge
- Functional enrichment, using human nodes from merged network
Proposed new workflow:
- Use cross-species query for human x HPV 16. Set the confidence score to ~0.5 or so to not get a huge network. HPV has 8 proteins (as far as I can tell)
- Skip Query for additional host proteins
- Merge networks.
- Functional enrichment
@scootermorris: Let me know if you have any feedback or if Im missing anything.
from cytoscape-tutorials.
Since there will be upcoming changes to the string app which will necessitate an overhaul of this tutorial, the solution is to comment out workflow 4 for now.
73d48e8
from cytoscape-tutorials.
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from cytoscape-tutorials.