Loading data into Cytoscape 3 from GenomeSpace

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In this video step, we will load some GenomeSpace data into the Cytoscape network visualizer tool. GenomeSpace allows us to move smoothly between tools. We will make use of this by visualizing the output from a GenePattern job.

In this video, I will demonstrate how to load data into Cytoscape 3 to create a network map. The input for this step is a gene list that has been filtered in GenePattern.

First, launch Cytoscape 3 from GenomeSpace by clicking the icon in the tool menu. This will download a JNLP file, which you can double-click to launch Cytoscape. If a warning message appears, check the box, and select "Run" to continue.

Once launched, select "With Empty Network" to load a new network. Feel free to change the name of the network, or simply leave as-is.

To navigate to the GenomeSpace import menu, click "File", "Import", "Network", and then "GenomeSpace".

This will open a window titled, "Import Network from Table". In this new window, select "Column 1" in the dropdown menu under "Source Interaction", then click "OK". Click "Yes" to continue if a warning message appears.

You have now loaded a network of gene nodes.
  1. GenomeSpace
  2. Genomespace
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