Genemania Cytoscape app (not local search): feedback from CBW pathway workshop in March 2019

[veroniquevoisin]

• search bar:
  

  • observed on 1 computer (windows) that a long gene list was covering the menu and search buttons on the right, it was impossible to start the search.

• parameters dialog box:
  

  • add the drug / transcription factor/ mir attributes
  • be able to upload a custom network
  • add an "OK" button at the right site of "Select Default" to apply selection and close the dialog box.

• additional features:

  • be able to color the nodes by function from results panels without going to 'style' and 'node color'.
  • be able to click on a node (gene) and see its related functions highlighted in yellow in Results Panel
  • be able to select a few nodes from network and rerun a search using selected nodes.

• layout:

  • be able to get the circular layout with the query genes in the center and related genes as a circle outside the query genes as in the genemania website

• export network:

  • be able to export the network to reconstitue it outside genemania to add other layer of information. Sif export is missing the edges informations (genemania network information) and the network table from Table Panel only displays one interaction even if all nodes are selected.

[veroniquevoisin]

Cytoscape 3.7.1 was used during this workshop

[maxkfranz]

be able to export the network to reconstitue it outside genemania to add other layer of information. Sif export is missing the edges informations (genemania network information) and the network table from Table Panel only displays one interaction even if all nodes are selected.

The JSON exporter might already include this.