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cytoscape / cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js
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Update stringApp tutorial #110

Closed khanspers closed 6 months ago

khanspers commented 6 months ago

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 6 months ago

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 6 months ago

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. https://github.com/cytoscape/cytoscape-tutorials/commit/73d48e8e30b6a8ccc7bc9dd02567ea2ec50a761d