cytoscape/cytoscape-tutorials

Update stringApp tutorial

khanspers opened this issue · 2 comments

khanspers commented

The last workflow needs updates since virus-host is now handled via cross-species "mode".
https://cytoscape.org/cytoscape-tutorials/protocols/stringApp/#/5/2

khanspers commented

Here are the steps of the current workflow, with comments:

  1. 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
  2. Expand network with human interactors (10) using "Apps>String>Expand network" => Can't do this since we don't have an HPV network.
  3. Add specific host proteins
  4. Repeat network import/expansion for HPV1a => same problem as before
  5. Merge
  6. Functional enrichment, using human nodes from merged network

Proposed new workflow:

  1. 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)
  2. Skip Query for additional host proteins
  3. Merge networks.
  4. Functional enrichment

@scootermorris: Let me know if you have any feedback or if Im missing anything.

khanspers commented

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