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TOPOLOGICAL FEATURES USING CYTOSCAPE 3.2.1 HOW TO

the recommended enrichmentmap version for Cytoscape 3.2 is the enrichmap version that contains the automatic annotation option (Release 2.1.0 ).more on java folders and set JAVA_HOME environment variable to Java 7 path.

TOPOLOGICAL FEATURES USING CYTOSCAPE 3.2.1 HOW TO

Use cytoscape 3.2.1 or later and latest EnrichmentMap version (built 627 or later) How to collapse group nodes into a single metanode (in order to simplify the map).

manual creation of groups and manual collapsing of nodes (1 by 1).

Right click on the selected nodes and choose the option "group" => "group selected nodes" => name it.double click on the group on the node to collapse it.to expand a metanode, double-click on it and the individual nodes forming the group will be displayed.Īdd automatic labels using the "Annotate Cluster" feature (in menu -> EnrichmentMap -> Annotate Cluster).Run the "Annotate Cluster" with the option "Create Groups for clusters" checked (Control Panel -> Annotation Panel -> Advanced Option -> Create Groups for clusters).once the metanodes are created, we can change their size, color, shapes as other nodes.How to create a signature gene-set to use with the post-analysis option of enrichmentmap We also can import attributes for these nodes.take the list of genes that you want to overlap with the map.