TIPS ON HOW TO USE ENRICHMENTMAP AND CYTOSCAPE (provided by the bioinformatics service and EnrichmentMap software developpers)

Description of the page:

• this page collects tips on how to use EnrichmentMap and Cytoscape based on frequently asked questions and known issues.

• it is based from received feedback from and tailored to the need of the OICR Cancer Stem Cell users (http://oicr.on.ca/oicr-programs-and-platforms/innovation-programs/cancer-stem-cell)

• do not hesitate to contact us if you need any assistance while executing these steps or have issues not reported on this page (veronique.voisin@gmail.com)

• for description on our workflow or how to create a maps, please visit these pages : http://www.baderlab.org/VeroniqueVoisin/Intranet/Protocol, http://www.baderlab.org/Software/EnrichmentMap

TIPS SECTION STARTS HERE:

Cytoscape 3.2

• will be officially released soon, please wait for update

• runs on java7 see instructions here: here if you have an older Snow Leopard 10.6.8

• you can use this script to upgrade your cytoscape 2.8 session files:convert_cyto_28_to_3_EM.sh or use the manual procedure described in the Cytoscape 3.1.1 section

• the recommended enrichmentmap version for Cytoscape 3.2 is the enrichmap version that contains the automatic annotation option (Release 2.1.0 (Beta 1))

Cytoscape 3.1.1

• recommended version of EnrichmentMap is 2.0.1 (Oct 5, 2014)

• runs on java 6 or 7

Open an existing enrichment map session file (.cys) (Oct 5, 2014)

• to fully open a stored session: open Cytoscape first and then the session file.

Create a figure (manual annotation) with an EnrichmentMap in Cytoscape 3.1.1 [Sept 23, 2014]

• How to create a figure with manual annotation of the functional modules (note: an automatic annotation function will be soon available for Cytoscape 3.2):
  1. Change the background to white:
     • in Control Panel

       • --> Style

         • --> at the bottom, select Network

           • --> Background Paint: choose the white color and click on OK

  2. remove the labels:
     • go to Table Panel

       • -> double check that you have the focus on Node Table

         • --> Click on the 5th Symbol item to create a "New Single Column" --> Integer

           • --> name this new column "no_labels"

     • go to Control Panel --> Style

       • make sure that the focus is on "Node" (at the bottom)

       • change Label --> Column to "no_labels"

  3. Export the network as a pdf:
     • arrange the nodes and the view as you would like them to appear on the figures (e.g red nodes on the left and blue nodes on the right)
     • Click on the icon "Export Image to File"

       • --> choose the PDF format, browse to your desired folder, choose a name and click on "OK"

  4. Open a powerpoint document and import the pdf file:

     • looking at the labels of single nodes or using the application WordCloud to look at the labels of a group of nodes, manually annotate the map on your powerpoint slide.

Move label position of nodes (Oct 5, 2014)

• go to Style in the Control Panel and click on the word "Properties" (it gives a list of all properties)

  • --> choose "Label Position" (this property is now added to the list) and double click on the first box (icon with a rectangle box) to move the labels to desired position)

    • 

Cytoscape 2.8

• To use Cytoscape 2.8, Cytoscape 2.8.3 and version of EnrichmentMap 1.3 is recommended (Sept 23, 2014)

• Cytoscape 2.8 runs with java6 only.
• It is recommended to use the latest version of Cytoscape (Cytoscape 3) to get benefits from new features (unless you can't upgrade to java 7 or 8).

If you have a project done with Cytoscape 2.8 and want to correctly open these files with Cytoscape 3 you can follow this procedure (recommended for experienced users only)(tips created on Sept 23, 2014):

How to make a Cytoscape 2.8 file compatible for Cytoscape 3 :

• open Cytoscape 3.1.1
• open the 2.8 file
• save the file with a new name (e.g. _cyto3)
• change the extension from .cys to .zip for both the old and new files
• unzip the old and new files

• copy the folder called Enrichment_Map_plugin (located in the plugins folder) from the old file to the Apps folder of the new file and call it EnrichmentMap (old cyto2.8 file/plugin/Enrichment_Map_plugin --> new cyto3 file/Apps/EnrichmentMap)

• zip the new session with a new name and replace the extension .zip to .cys

  • zip -r DP_ImmGeneUP_nov18_2013_cyto3_emadded.zip CytoscapeSession-2014_09_18-09_44

  • mv DP_ImmGeneUP_nov18_2013_cyto3_emadded.zip DP_ImmGeneUP_nov18_2013_cyto3_emadded.cys

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