Pathways visualization as network

Question

[oriolebaltimore]

Hi, Using C2 pathways from Msigdb, can I draw a cytoscape type network In this each node would be a pathway and edges represent strength of overlap of genes in that pathway. I am aware that this can be done using enrichment map app in cytoscape. However, my question is can it be done without enrichment metrics. I have only list of c2 pathway sets. Thanks Adrian

Answer 1

[ruth.isserlin]

You used to be able to create an enrichment map with just a gmt file but looks like that feature has disappeared in the current release (I am not sure at what point it disappeared). I have added it as a bug in our issue tracker. Hopefully it will get added back in - https://github.com/BaderLab/EnrichmentMapApp/issues/473

Currently the only way to do it would be to create a fake enrichment result file with all the pathways in the gmt file with fake p-values and q-values.

[ruth.isserlin]

Sorry, the feature is still there. If you add a dataset and only specify the gmt file then Enrichment map will be built with just the pathway definitions.